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| a | b/notebooks/mapping_zebrafish.ipynb | ||
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| 1 | { |
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| 2 | "cells": [ |
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| 3 | { |
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| 4 | "cell_type": "code", |
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| 5 | "execution_count": 1, |
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| 6 | "metadata": {}, |
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| 7 | "outputs": [], |
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| 8 | "source": [ |
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| 9 | "%load_ext autoreload\n", |
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| 10 | "%autoreload 2\n", |
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| 11 | "\n", |
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| 12 | "%matplotlib inline" |
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| 13 | ] |
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| 14 | }, |
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| 15 | { |
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| 16 | "cell_type": "code", |
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| 17 | "execution_count": 2, |
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| 18 | "metadata": {}, |
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| 19 | "outputs": [], |
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| 20 | "source": [ |
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| 21 | "import os, sys" |
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| 22 | ] |
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| 23 | }, |
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| 24 | { |
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| 25 | "cell_type": "code", |
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| 26 | "execution_count": 3, |
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| 27 | "metadata": {}, |
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| 28 | "outputs": [], |
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| 29 | "source": [ |
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| 30 | "import pandas as pd" |
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| 31 | ] |
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| 32 | }, |
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| 33 | { |
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| 34 | "cell_type": "code", |
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| 35 | "execution_count": 4, |
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| 36 | "metadata": {}, |
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| 37 | "outputs": [ |
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| 38 | { |
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| 39 | "name": "stderr", |
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| 40 | "output_type": "stream", |
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| 41 | "text": [ |
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| 42 | "2022-03-24 14:40:16.457 | WARNING | pyMultiOmics.reactome:get_neo4j_driver:14 - Using a default neo4j server: bolt://localhost:7687\n", |
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| 43 | "2022-03-24 14:40:16.458 | WARNING | pyMultiOmics.reactome:get_neo4j_driver:19 - Using a default neo4j username or password: neo4j\n", |
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| 44 | "2022-03-24 14:40:16.459 | INFO | pyMultiOmics.reactome:get_neo4j_driver:24 - Created graph database driver for bolt://localhost:7687 (neo4j)\n" |
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| 45 | ] |
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| 46 | } |
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| 47 | ], |
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| 48 | "source": [ |
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| 49 | "sys.path.append('..')\n", |
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| 50 | "\n", |
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| 51 | "from pyMultiOmics.base import SingleOmicsData, MultiOmicsData\n", |
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| 52 | "from pyMultiOmics.constants import GENES, PROTEINS, COMPOUNDS, DANIO_RERIO, REACTIONS, PATHWAYS\n", |
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| 53 | "from pyMultiOmics.mapping import Mapper\n", |
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| 54 | "from pyMultiOmics.common import set_log_level_info, set_log_level_debug, download_file, extract_zip_file" |
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| 55 | ] |
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| 56 | }, |
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| 57 | { |
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| 58 | "cell_type": "markdown", |
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| 59 | "metadata": {}, |
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| 60 | "source": [ |
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| 61 | "# Demonstration of pyMultiOmics mapping" |
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| 62 | ] |
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| 63 | }, |
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| 64 | { |
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| 65 | "cell_type": "markdown", |
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| 66 | "metadata": {}, |
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| 67 | "source": [ |
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| 68 | "## Load the processed Zebrafish data from [1]\n", |
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| 69 | "\n", |
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| 70 | "[1] [Rabinowitz, Jeremy S., et al. \"Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish.\" Proceedings of the National Academy of Sciences 114.5 (2017): E717-E726.](https://www.pnas.org/content/114/5/E717.short)" |
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| 71 | ] |
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| 72 | }, |
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| 73 | { |
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| 74 | "cell_type": "code", |
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| 75 | "execution_count": 5, |
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| 76 | "metadata": {}, |
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| 77 | "outputs": [ |
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| 78 | { |
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| 79 | "name": "stderr", |
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| 80 | "output_type": "stream", |
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| 81 | "text": [ |
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| 82 | "2022-03-24 14:40:25.643 | INFO | pyMultiOmics.common:download_file:59 - Downloading zebrafish_data.zip\n", |
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| 83 | "1.75kKB [00:00, 22.0kKB/s] \n", |
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| 84 | "2022-03-24 14:40:25.771 | INFO | pyMultiOmics.common:extract_zip_file:71 - Extracting zebrafish_data.zip\n", |
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| 85 | "100%|██████████████████████████████████████████████████████████████████████████████████| 17/17 [00:00<00:00, 349.96it/s]\n", |
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| 86 | "2022-03-24 14:40:25.823 | INFO | pyMultiOmics.common:extract_zip_file:77 - Deleting zebrafish_data.zip\n" |
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| 87 | ] |
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| 88 | } |
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| 89 | ], |
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| 90 | "source": [ |
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| 91 | "url = 'https://github.com/glasgowcompbio/pyMultiOmics-data/raw/main/zebrafish_data.zip'\n", |
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| 92 | "out_file = download_file(url)\n", |
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| 93 | "extract_zip_file(out_file)" |
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| 94 | ] |
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| 95 | }, |
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| 96 | { |
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| 97 | "cell_type": "code", |
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| 98 | "execution_count": 6, |
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| 99 | "metadata": {}, |
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| 100 | "outputs": [ |
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| 101 | { |
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| 102 | "data": { |
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| 103 | "text/plain": [ |
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| 104 | "'/Users/joewandy/Work/git/pyMultiOmics/notebooks/zebrafish_data'" |
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| 105 | ] |
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| 106 | }, |
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| 107 | "execution_count": 6, |
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| 108 | "metadata": {}, |
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| 109 | "output_type": "execute_result" |
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| 110 | } |
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| 111 | ], |
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| 112 | "source": [ |
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| 113 | "DATA_FOLDER = os.path.abspath(os.path.join('zebrafish_data'))\n", |
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| 114 | "DATA_FOLDER" |
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| 115 | ] |
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| 116 | }, |
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| 117 | { |
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| 118 | "cell_type": "markdown", |
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| 119 | "metadata": {}, |
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| 120 | "source": [ |
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| 121 | "Read transcriptomics data (identified by their gene ids)" |
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| 122 | ] |
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| 123 | }, |
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| 124 | { |
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| 125 | "cell_type": "code", |
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| 126 | "execution_count": 7, |
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| 127 | "metadata": {}, |
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| 128 | "outputs": [], |
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| 129 | "source": [ |
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| 130 | "gene_data = pd.read_csv(os.path.join(DATA_FOLDER, 'gene_data_combined.csv'), index_col='Identifier')\n", |
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| 131 | "gene_design = pd.read_csv(os.path.join(DATA_FOLDER, 'gene_design.csv'), index_col='sample')" |
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| 132 | ] |
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| 133 | }, |
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| 134 | { |
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| 135 | "cell_type": "code", |
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| 136 | "execution_count": 8, |
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| 137 | "metadata": {}, |
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| 138 | "outputs": [ |
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| 139 | { |
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| 140 | "data": { |
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| 157 | " <thead>\n", |
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| 334 | " US-1584693 US-1584700 US-1584706 US-1584712 \\\n", |
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| 389 | "\n", |
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| 390 | "[5 rows x 21 columns]" |
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| 391 | ] |
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| 392 | }, |
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| 393 | "execution_count": 8, |
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| 394 | "metadata": {}, |
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| 395 | "output_type": "execute_result" |
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| 396 | } |
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| 397 | ], |
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| 398 | "source": [ |
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| 399 | "gene_data.head()" |
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| 400 | ] |
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| 401 | }, |
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| 402 | { |
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| 404 | "execution_count": 9, |
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| 405 | "metadata": {}, |
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| 427 | " <th></th>\n", |
||
| 428 | " <th>group</th>\n", |
||
| 429 | " </tr>\n", |
||
| 430 | " <tr>\n", |
||
| 431 | " <th>sample</th>\n", |
||
| 432 | " <th></th>\n", |
||
| 433 | " </tr>\n", |
||
| 434 | " </thead>\n", |
||
| 435 | " <tbody>\n", |
||
| 436 | " <tr>\n", |
||
| 437 | " <th>US-1584752</th>\n", |
||
| 438 | " <td>Proximal</td>\n", |
||
| 439 | " </tr>\n", |
||
| 440 | " <tr>\n", |
||
| 441 | " <th>US-1584732</th>\n", |
||
| 442 | " <td>Proximal</td>\n", |
||
| 443 | " </tr>\n", |
||
| 444 | " <tr>\n", |
||
| 445 | " <th>US-1584724</th>\n", |
||
| 446 | " <td>Proximal</td>\n", |
||
| 447 | " </tr>\n", |
||
| 448 | " <tr>\n", |
||
| 449 | " <th>US-1584693</th>\n", |
||
| 450 | " <td>Proximal</td>\n", |
||
| 451 | " </tr>\n", |
||
| 452 | " <tr>\n", |
||
| 453 | " <th>US-1584758</th>\n", |
||
| 454 | " <td>Proximal</td>\n", |
||
| 455 | " </tr>\n", |
||
| 456 | " <tr>\n", |
||
| 457 | " <th>US-1584725</th>\n", |
||
| 458 | " <td>Middle</td>\n", |
||
| 459 | " </tr>\n", |
||
| 460 | " <tr>\n", |
||
| 461 | " <th>US-1584706</th>\n", |
||
| 462 | " <td>Middle</td>\n", |
||
| 463 | " </tr>\n", |
||
| 464 | " <tr>\n", |
||
| 465 | " <th>US-1584700</th>\n", |
||
| 466 | " <td>Middle</td>\n", |
||
| 467 | " </tr>\n", |
||
| 468 | " <tr>\n", |
||
| 469 | " <th>US-1584744</th>\n", |
||
| 470 | " <td>Middle</td>\n", |
||
| 471 | " </tr>\n", |
||
| 472 | " <tr>\n", |
||
| 473 | " <th>US-1584753</th>\n", |
||
| 474 | " <td>Middle</td>\n", |
||
| 475 | " </tr>\n", |
||
| 476 | " <tr>\n", |
||
| 477 | " <th>US-1584738</th>\n", |
||
| 478 | " <td>Distal</td>\n", |
||
| 479 | " </tr>\n", |
||
| 480 | " <tr>\n", |
||
| 481 | " <th>US-1584722</th>\n", |
||
| 482 | " <td>Distal</td>\n", |
||
| 483 | " </tr>\n", |
||
| 484 | " <tr>\n", |
||
| 485 | " <th>US-1584712</th>\n", |
||
| 486 | " <td>Distal</td>\n", |
||
| 487 | " </tr>\n", |
||
| 488 | " <tr>\n", |
||
| 489 | " <th>US-1584754</th>\n", |
||
| 490 | " <td>Distal</td>\n", |
||
| 491 | " </tr>\n", |
||
| 492 | " <tr>\n", |
||
| 493 | " <th>US-1584765</th>\n", |
||
| 494 | " <td>Distal</td>\n", |
||
| 495 | " </tr>\n", |
||
| 496 | " </tbody>\n", |
||
| 497 | "</table>\n", |
||
| 498 | "</div>" |
||
| 499 | ], |
||
| 500 | "text/plain": [ |
||
| 501 | " group\n", |
||
| 502 | "sample \n", |
||
| 503 | "US-1584752 Proximal\n", |
||
| 504 | "US-1584732 Proximal\n", |
||
| 505 | "US-1584724 Proximal\n", |
||
| 506 | "US-1584693 Proximal\n", |
||
| 507 | "US-1584758 Proximal\n", |
||
| 508 | "US-1584725 Middle\n", |
||
| 509 | "US-1584706 Middle\n", |
||
| 510 | "US-1584700 Middle\n", |
||
| 511 | "US-1584744 Middle\n", |
||
| 512 | "US-1584753 Middle\n", |
||
| 513 | "US-1584738 Distal\n", |
||
| 514 | "US-1584722 Distal\n", |
||
| 515 | "US-1584712 Distal\n", |
||
| 516 | "US-1584754 Distal\n", |
||
| 517 | "US-1584765 Distal" |
||
| 518 | ] |
||
| 519 | }, |
||
| 520 | "execution_count": 9, |
||
| 521 | "metadata": {}, |
||
| 522 | "output_type": "execute_result" |
||
| 523 | } |
||
| 524 | ], |
||
| 525 | "source": [ |
||
| 526 | "gene_design" |
||
| 527 | ] |
||
| 528 | }, |
||
| 529 | { |
||
| 530 | "cell_type": "markdown", |
||
| 531 | "metadata": {}, |
||
| 532 | "source": [ |
||
| 533 | "Read proteomics data" |
||
| 534 | ] |
||
| 535 | }, |
||
| 536 | { |
||
| 537 | "cell_type": "code", |
||
| 538 | "execution_count": 10, |
||
| 539 | "metadata": {}, |
||
| 540 | "outputs": [], |
||
| 541 | "source": [ |
||
| 542 | "protein_data = pd.read_csv(os.path.join(DATA_FOLDER, 'protein_data.csv'), index_col='Uniprot')\n", |
||
| 543 | "protein_design = pd.read_csv(os.path.join(DATA_FOLDER, 'protein_design.csv'), index_col='sample')" |
||
| 544 | ] |
||
| 545 | }, |
||
| 546 | { |
||
| 547 | "cell_type": "code", |
||
| 548 | "execution_count": 11, |
||
| 549 | "metadata": {}, |
||
| 550 | "outputs": [ |
||
| 551 | { |
||
| 552 | "data": { |
||
| 553 | "text/html": [ |
||
| 554 | "<div>\n", |
||
| 555 | "<style scoped>\n", |
||
| 556 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 557 | " vertical-align: middle;\n", |
||
| 558 | " }\n", |
||
| 559 | "\n", |
||
| 560 | " .dataframe tbody tr th {\n", |
||
| 561 | " vertical-align: top;\n", |
||
| 562 | " }\n", |
||
| 563 | "\n", |
||
| 564 | " .dataframe thead th {\n", |
||
| 565 | " text-align: right;\n", |
||
| 566 | " }\n", |
||
| 567 | "</style>\n", |
||
| 568 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 569 | " <thead>\n", |
||
| 570 | " <tr style=\"text-align: right;\">\n", |
||
| 571 | " <th></th>\n", |
||
| 572 | " <th>Distal#3_01</th>\n", |
||
| 573 | " <th>Distal#3_02</th>\n", |
||
| 574 | " <th>Distal#3_03</th>\n", |
||
| 575 | " <th>Distal#3_04</th>\n", |
||
| 576 | " <th>Middle#3_01</th>\n", |
||
| 577 | " <th>Middle#3_02</th>\n", |
||
| 578 | " <th>Middle#3_03</th>\n", |
||
| 579 | " <th>Middle#3_04</th>\n", |
||
| 580 | " <th>Proximal#3_01</th>\n", |
||
| 581 | " <th>Proximal#3_02</th>\n", |
||
| 582 | " <th>Proximal#3_03</th>\n", |
||
| 583 | " <th>Proximal#3_04</th>\n", |
||
| 584 | " </tr>\n", |
||
| 585 | " <tr>\n", |
||
| 586 | " <th>Uniprot</th>\n", |
||
| 587 | " <th></th>\n", |
||
| 588 | " <th></th>\n", |
||
| 589 | " <th></th>\n", |
||
| 590 | " <th></th>\n", |
||
| 591 | " <th></th>\n", |
||
| 592 | " <th></th>\n", |
||
| 593 | " <th></th>\n", |
||
| 594 | " <th></th>\n", |
||
| 595 | " <th></th>\n", |
||
| 596 | " <th></th>\n", |
||
| 597 | " <th></th>\n", |
||
| 598 | " <th></th>\n", |
||
| 599 | " </tr>\n", |
||
| 600 | " </thead>\n", |
||
| 601 | " <tbody>\n", |
||
| 602 | " <tr>\n", |
||
| 603 | " <th>A0A0A0MPL4</th>\n", |
||
| 604 | " <td>9.955264e+05</td>\n", |
||
| 605 | " <td>4.946580e+06</td>\n", |
||
| 606 | " <td>1.377194e+06</td>\n", |
||
| 607 | " <td>2.208140e+06</td>\n", |
||
| 608 | " <td>2.907807e+06</td>\n", |
||
| 609 | " <td>4.231976e+06</td>\n", |
||
| 610 | " <td>1.560849e+06</td>\n", |
||
| 611 | " <td>2.852904e+06</td>\n", |
||
| 612 | " <td>1781795.086</td>\n", |
||
| 613 | " <td>2.668135e+06</td>\n", |
||
| 614 | " <td>3.079148e+06</td>\n", |
||
| 615 | " <td>2.840473e+06</td>\n", |
||
| 616 | " </tr>\n", |
||
| 617 | " <tr>\n", |
||
| 618 | " <th>A0A0B4J1A5</th>\n", |
||
| 619 | " <td>2.982519e+06</td>\n", |
||
| 620 | " <td>8.816655e+06</td>\n", |
||
| 621 | " <td>7.668431e+06</td>\n", |
||
| 622 | " <td>4.632309e+06</td>\n", |
||
| 623 | " <td>7.672153e+06</td>\n", |
||
| 624 | " <td>7.776017e+06</td>\n", |
||
| 625 | " <td>6.633781e+06</td>\n", |
||
| 626 | " <td>8.242783e+06</td>\n", |
||
| 627 | " <td>5475654.544</td>\n", |
||
| 628 | " <td>5.703832e+06</td>\n", |
||
| 629 | " <td>8.294364e+06</td>\n", |
||
| 630 | " <td>1.334874e+07</td>\n", |
||
| 631 | " </tr>\n", |
||
| 632 | " <tr>\n", |
||
| 633 | " <th>A0A0B4J1A7</th>\n", |
||
| 634 | " <td>1.553049e+07</td>\n", |
||
| 635 | " <td>1.037155e+06</td>\n", |
||
| 636 | " <td>1.856137e+07</td>\n", |
||
| 637 | " <td>1.767859e+07</td>\n", |
||
| 638 | " <td>1.375736e+07</td>\n", |
||
| 639 | " <td>1.747998e+07</td>\n", |
||
| 640 | " <td>1.517507e+07</td>\n", |
||
| 641 | " <td>2.394465e+07</td>\n", |
||
| 642 | " <td>3157387.719</td>\n", |
||
| 643 | " <td>1.794775e+07</td>\n", |
||
| 644 | " <td>2.300430e+07</td>\n", |
||
| 645 | " <td>2.063800e+07</td>\n", |
||
| 646 | " </tr>\n", |
||
| 647 | " <tr>\n", |
||
| 648 | " <th>A0AUQ3</th>\n", |
||
| 649 | " <td>2.012699e+06</td>\n", |
||
| 650 | " <td>3.088982e+06</td>\n", |
||
| 651 | " <td>2.455865e+06</td>\n", |
||
| 652 | " <td>9.448331e+05</td>\n", |
||
| 653 | " <td>2.866780e+06</td>\n", |
||
| 654 | " <td>2.661669e+06</td>\n", |
||
| 655 | " <td>2.100352e+06</td>\n", |
||
| 656 | " <td>2.133662e+06</td>\n", |
||
| 657 | " <td>1738244.989</td>\n", |
||
| 658 | " <td>2.629396e+06</td>\n", |
||
| 659 | " <td>2.900560e+06</td>\n", |
||
| 660 | " <td>2.416018e+06</td>\n", |
||
| 661 | " </tr>\n", |
||
| 662 | " <tr>\n", |
||
| 663 | " <th>A0AUR9</th>\n", |
||
| 664 | " <td>3.640487e+06</td>\n", |
||
| 665 | " <td>2.588477e+07</td>\n", |
||
| 666 | " <td>3.415989e+07</td>\n", |
||
| 667 | " <td>2.868569e+06</td>\n", |
||
| 668 | " <td>1.971142e+06</td>\n", |
||
| 669 | " <td>2.472776e+06</td>\n", |
||
| 670 | " <td>5.615177e+06</td>\n", |
||
| 671 | " <td>1.303356e+06</td>\n", |
||
| 672 | " <td>3263299.566</td>\n", |
||
| 673 | " <td>6.866769e+06</td>\n", |
||
| 674 | " <td>2.465929e+06</td>\n", |
||
| 675 | " <td>4.515643e+06</td>\n", |
||
| 676 | " </tr>\n", |
||
| 677 | " </tbody>\n", |
||
| 678 | "</table>\n", |
||
| 679 | "</div>" |
||
| 680 | ], |
||
| 681 | "text/plain": [ |
||
| 682 | " Distal#3_01 Distal#3_02 Distal#3_03 Distal#3_04 \\\n", |
||
| 683 | "Uniprot \n", |
||
| 684 | "A0A0A0MPL4 9.955264e+05 4.946580e+06 1.377194e+06 2.208140e+06 \n", |
||
| 685 | "A0A0B4J1A5 2.982519e+06 8.816655e+06 7.668431e+06 4.632309e+06 \n", |
||
| 686 | "A0A0B4J1A7 1.553049e+07 1.037155e+06 1.856137e+07 1.767859e+07 \n", |
||
| 687 | "A0AUQ3 2.012699e+06 3.088982e+06 2.455865e+06 9.448331e+05 \n", |
||
| 688 | "A0AUR9 3.640487e+06 2.588477e+07 3.415989e+07 2.868569e+06 \n", |
||
| 689 | "\n", |
||
| 690 | " Middle#3_01 Middle#3_02 Middle#3_03 Middle#3_04 \\\n", |
||
| 691 | "Uniprot \n", |
||
| 692 | "A0A0A0MPL4 2.907807e+06 4.231976e+06 1.560849e+06 2.852904e+06 \n", |
||
| 693 | "A0A0B4J1A5 7.672153e+06 7.776017e+06 6.633781e+06 8.242783e+06 \n", |
||
| 694 | "A0A0B4J1A7 1.375736e+07 1.747998e+07 1.517507e+07 2.394465e+07 \n", |
||
| 695 | "A0AUQ3 2.866780e+06 2.661669e+06 2.100352e+06 2.133662e+06 \n", |
||
| 696 | "A0AUR9 1.971142e+06 2.472776e+06 5.615177e+06 1.303356e+06 \n", |
||
| 697 | "\n", |
||
| 698 | " Proximal#3_01 Proximal#3_02 Proximal#3_03 Proximal#3_04 \n", |
||
| 699 | "Uniprot \n", |
||
| 700 | "A0A0A0MPL4 1781795.086 2.668135e+06 3.079148e+06 2.840473e+06 \n", |
||
| 701 | "A0A0B4J1A5 5475654.544 5.703832e+06 8.294364e+06 1.334874e+07 \n", |
||
| 702 | "A0A0B4J1A7 3157387.719 1.794775e+07 2.300430e+07 2.063800e+07 \n", |
||
| 703 | "A0AUQ3 1738244.989 2.629396e+06 2.900560e+06 2.416018e+06 \n", |
||
| 704 | "A0AUR9 3263299.566 6.866769e+06 2.465929e+06 4.515643e+06 " |
||
| 705 | ] |
||
| 706 | }, |
||
| 707 | "execution_count": 11, |
||
| 708 | "metadata": {}, |
||
| 709 | "output_type": "execute_result" |
||
| 710 | } |
||
| 711 | ], |
||
| 712 | "source": [ |
||
| 713 | "protein_data.head()" |
||
| 714 | ] |
||
| 715 | }, |
||
| 716 | { |
||
| 717 | "cell_type": "code", |
||
| 718 | "execution_count": 12, |
||
| 719 | "metadata": {}, |
||
| 720 | "outputs": [ |
||
| 721 | { |
||
| 722 | "data": { |
||
| 723 | "text/html": [ |
||
| 724 | "<div>\n", |
||
| 725 | "<style scoped>\n", |
||
| 726 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 727 | " vertical-align: middle;\n", |
||
| 728 | " }\n", |
||
| 729 | "\n", |
||
| 730 | " .dataframe tbody tr th {\n", |
||
| 731 | " vertical-align: top;\n", |
||
| 732 | " }\n", |
||
| 733 | "\n", |
||
| 734 | " .dataframe thead th {\n", |
||
| 735 | " text-align: right;\n", |
||
| 736 | " }\n", |
||
| 737 | "</style>\n", |
||
| 738 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 739 | " <thead>\n", |
||
| 740 | " <tr style=\"text-align: right;\">\n", |
||
| 741 | " <th></th>\n", |
||
| 742 | " <th>group</th>\n", |
||
| 743 | " </tr>\n", |
||
| 744 | " <tr>\n", |
||
| 745 | " <th>sample</th>\n", |
||
| 746 | " <th></th>\n", |
||
| 747 | " </tr>\n", |
||
| 748 | " </thead>\n", |
||
| 749 | " <tbody>\n", |
||
| 750 | " <tr>\n", |
||
| 751 | " <th>Distal#3_01</th>\n", |
||
| 752 | " <td>Distal</td>\n", |
||
| 753 | " </tr>\n", |
||
| 754 | " <tr>\n", |
||
| 755 | " <th>Distal#3_02</th>\n", |
||
| 756 | " <td>Distal</td>\n", |
||
| 757 | " </tr>\n", |
||
| 758 | " <tr>\n", |
||
| 759 | " <th>Distal#3_03</th>\n", |
||
| 760 | " <td>Distal</td>\n", |
||
| 761 | " </tr>\n", |
||
| 762 | " <tr>\n", |
||
| 763 | " <th>Distal#3_04</th>\n", |
||
| 764 | " <td>Distal</td>\n", |
||
| 765 | " </tr>\n", |
||
| 766 | " <tr>\n", |
||
| 767 | " <th>Middle#3_01</th>\n", |
||
| 768 | " <td>Middle</td>\n", |
||
| 769 | " </tr>\n", |
||
| 770 | " <tr>\n", |
||
| 771 | " <th>Middle#3_02</th>\n", |
||
| 772 | " <td>Middle</td>\n", |
||
| 773 | " </tr>\n", |
||
| 774 | " <tr>\n", |
||
| 775 | " <th>Middle#3_03</th>\n", |
||
| 776 | " <td>Middle</td>\n", |
||
| 777 | " </tr>\n", |
||
| 778 | " <tr>\n", |
||
| 779 | " <th>Middle#3_04</th>\n", |
||
| 780 | " <td>Middle</td>\n", |
||
| 781 | " </tr>\n", |
||
| 782 | " <tr>\n", |
||
| 783 | " <th>Proximal#3_01</th>\n", |
||
| 784 | " <td>Proximal</td>\n", |
||
| 785 | " </tr>\n", |
||
| 786 | " <tr>\n", |
||
| 787 | " <th>Proximal#3_02</th>\n", |
||
| 788 | " <td>Proximal</td>\n", |
||
| 789 | " </tr>\n", |
||
| 790 | " <tr>\n", |
||
| 791 | " <th>Proximal#3_03</th>\n", |
||
| 792 | " <td>Proximal</td>\n", |
||
| 793 | " </tr>\n", |
||
| 794 | " <tr>\n", |
||
| 795 | " <th>Proximal#3_04</th>\n", |
||
| 796 | " <td>Proximal</td>\n", |
||
| 797 | " </tr>\n", |
||
| 798 | " </tbody>\n", |
||
| 799 | "</table>\n", |
||
| 800 | "</div>" |
||
| 801 | ], |
||
| 802 | "text/plain": [ |
||
| 803 | " group\n", |
||
| 804 | "sample \n", |
||
| 805 | "Distal#3_01 Distal\n", |
||
| 806 | "Distal#3_02 Distal\n", |
||
| 807 | "Distal#3_03 Distal\n", |
||
| 808 | "Distal#3_04 Distal\n", |
||
| 809 | "Middle#3_01 Middle\n", |
||
| 810 | "Middle#3_02 Middle\n", |
||
| 811 | "Middle#3_03 Middle\n", |
||
| 812 | "Middle#3_04 Middle\n", |
||
| 813 | "Proximal#3_01 Proximal\n", |
||
| 814 | "Proximal#3_02 Proximal\n", |
||
| 815 | "Proximal#3_03 Proximal\n", |
||
| 816 | "Proximal#3_04 Proximal" |
||
| 817 | ] |
||
| 818 | }, |
||
| 819 | "execution_count": 12, |
||
| 820 | "metadata": {}, |
||
| 821 | "output_type": "execute_result" |
||
| 822 | } |
||
| 823 | ], |
||
| 824 | "source": [ |
||
| 825 | "protein_design" |
||
| 826 | ] |
||
| 827 | }, |
||
| 828 | { |
||
| 829 | "cell_type": "markdown", |
||
| 830 | "metadata": {}, |
||
| 831 | "source": [ |
||
| 832 | "Read metabolomics data" |
||
| 833 | ] |
||
| 834 | }, |
||
| 835 | { |
||
| 836 | "cell_type": "code", |
||
| 837 | "execution_count": 13, |
||
| 838 | "metadata": {}, |
||
| 839 | "outputs": [], |
||
| 840 | "source": [ |
||
| 841 | "compound_data = pd.read_csv(os.path.join(DATA_FOLDER, 'compound_data_kegg.csv'), index_col='Identifier')\n", |
||
| 842 | "compound_design = pd.read_csv(os.path.join(DATA_FOLDER, 'compound_design.csv'), index_col='sample')" |
||
| 843 | ] |
||
| 844 | }, |
||
| 845 | { |
||
| 846 | "cell_type": "code", |
||
| 847 | "execution_count": 14, |
||
| 848 | "metadata": {}, |
||
| 849 | "outputs": [ |
||
| 850 | { |
||
| 851 | "data": { |
||
| 852 | "text/html": [ |
||
| 853 | "<div>\n", |
||
| 854 | "<style scoped>\n", |
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| 855 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 856 | " vertical-align: middle;\n", |
||
| 857 | " }\n", |
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| 858 | "\n", |
||
| 859 | " .dataframe tbody tr th {\n", |
||
| 860 | " vertical-align: top;\n", |
||
| 861 | " }\n", |
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| 862 | "\n", |
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| 863 | " .dataframe thead th {\n", |
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| 864 | " text-align: right;\n", |
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| 865 | " }\n", |
||
| 866 | "</style>\n", |
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| 867 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 868 | " <thead>\n", |
||
| 869 | " <tr style=\"text-align: right;\">\n", |
||
| 870 | " <th></th>\n", |
||
| 871 | " <th>distal_M1</th>\n", |
||
| 872 | " <th>distal_M2</th>\n", |
||
| 873 | " <th>distal_M3</th>\n", |
||
| 874 | " <th>distal_F1</th>\n", |
||
| 875 | " <th>distal_F2</th>\n", |
||
| 876 | " <th>distal_F3</th>\n", |
||
| 877 | " <th>middle_M1</th>\n", |
||
| 878 | " <th>middle_M2</th>\n", |
||
| 879 | " <th>middle_M3</th>\n", |
||
| 880 | " <th>middle_F1</th>\n", |
||
| 881 | " <th>middle_F2</th>\n", |
||
| 882 | " <th>middle_F3</th>\n", |
||
| 883 | " <th>proximal_M1</th>\n", |
||
| 884 | " <th>proximal_M2</th>\n", |
||
| 885 | " <th>proximal_M3</th>\n", |
||
| 886 | " <th>proximal_F1</th>\n", |
||
| 887 | " <th>proximal_F2</th>\n", |
||
| 888 | " <th>proximal_F3</th>\n", |
||
| 889 | " </tr>\n", |
||
| 890 | " <tr>\n", |
||
| 891 | " <th>Identifier</th>\n", |
||
| 892 | " <th></th>\n", |
||
| 893 | " <th></th>\n", |
||
| 894 | " <th></th>\n", |
||
| 895 | " <th></th>\n", |
||
| 896 | " <th></th>\n", |
||
| 897 | " <th></th>\n", |
||
| 898 | " <th></th>\n", |
||
| 899 | " <th></th>\n", |
||
| 900 | " <th></th>\n", |
||
| 901 | " <th></th>\n", |
||
| 902 | " <th></th>\n", |
||
| 903 | " <th></th>\n", |
||
| 904 | " <th></th>\n", |
||
| 905 | " <th></th>\n", |
||
| 906 | " <th></th>\n", |
||
| 907 | " <th></th>\n", |
||
| 908 | " <th></th>\n", |
||
| 909 | " <th></th>\n", |
||
| 910 | " </tr>\n", |
||
| 911 | " </thead>\n", |
||
| 912 | " <tbody>\n", |
||
| 913 | " <tr>\n", |
||
| 914 | " <th>C00565</th>\n", |
||
| 915 | " <td>75170.0</td>\n", |
||
| 916 | " <td>57052</td>\n", |
||
| 917 | " <td>39170.0</td>\n", |
||
| 918 | " <td>84057</td>\n", |
||
| 919 | " <td>38608.0</td>\n", |
||
| 920 | " <td>64126.0</td>\n", |
||
| 921 | " <td>50214.0</td>\n", |
||
| 922 | " <td>75680</td>\n", |
||
| 923 | " <td>165178</td>\n", |
||
| 924 | " <td>121856</td>\n", |
||
| 925 | " <td>77061</td>\n", |
||
| 926 | " <td>98015.0</td>\n", |
||
| 927 | " <td>113765</td>\n", |
||
| 928 | " <td>96098</td>\n", |
||
| 929 | " <td>84198</td>\n", |
||
| 930 | " <td>117644</td>\n", |
||
| 931 | " <td>169459</td>\n", |
||
| 932 | " <td>169669</td>\n", |
||
| 933 | " </tr>\n", |
||
| 934 | " <tr>\n", |
||
| 935 | " <th>C00037</th>\n", |
||
| 936 | " <td>64511.0</td>\n", |
||
| 937 | " <td>33658</td>\n", |
||
| 938 | " <td>23565.0</td>\n", |
||
| 939 | " <td>52102</td>\n", |
||
| 940 | " <td>49508.0</td>\n", |
||
| 941 | " <td>37498.0</td>\n", |
||
| 942 | " <td>30417.0</td>\n", |
||
| 943 | " <td>55728</td>\n", |
||
| 944 | " <td>88519</td>\n", |
||
| 945 | " <td>103871</td>\n", |
||
| 946 | " <td>45974</td>\n", |
||
| 947 | " <td>73101.0</td>\n", |
||
| 948 | " <td>72725</td>\n", |
||
| 949 | " <td>66008</td>\n", |
||
| 950 | " <td>54220</td>\n", |
||
| 951 | " <td>95341</td>\n", |
||
| 952 | " <td>110192</td>\n", |
||
| 953 | " <td>291598</td>\n", |
||
| 954 | " </tr>\n", |
||
| 955 | " <tr>\n", |
||
| 956 | " <th>C01104</th>\n", |
||
| 957 | " <td>5787534.0</td>\n", |
||
| 958 | " <td>4351239</td>\n", |
||
| 959 | " <td>4401036.0</td>\n", |
||
| 960 | " <td>8187282</td>\n", |
||
| 961 | " <td>8431125.0</td>\n", |
||
| 962 | " <td>5082056.0</td>\n", |
||
| 963 | " <td>5138937.0</td>\n", |
||
| 964 | " <td>7341351</td>\n", |
||
| 965 | " <td>7837293</td>\n", |
||
| 966 | " <td>9256269</td>\n", |
||
| 967 | " <td>9934066</td>\n", |
||
| 968 | " <td>10243285.0</td>\n", |
||
| 969 | " <td>7344406</td>\n", |
||
| 970 | " <td>5524811</td>\n", |
||
| 971 | " <td>4809250</td>\n", |
||
| 972 | " <td>9279874</td>\n", |
||
| 973 | " <td>9047339</td>\n", |
||
| 974 | " <td>9211255</td>\n", |
||
| 975 | " </tr>\n", |
||
| 976 | " <tr>\n", |
||
| 977 | " <th>C00134</th>\n", |
||
| 978 | " <td>3430897.0</td>\n", |
||
| 979 | " <td>1877785</td>\n", |
||
| 980 | " <td>1225710.0</td>\n", |
||
| 981 | " <td>2326620</td>\n", |
||
| 982 | " <td>2421267.0</td>\n", |
||
| 983 | " <td>2595529.0</td>\n", |
||
| 984 | " <td>2003627.0</td>\n", |
||
| 985 | " <td>2120053</td>\n", |
||
| 986 | " <td>2269318</td>\n", |
||
| 987 | " <td>3220850</td>\n", |
||
| 988 | " <td>4596854</td>\n", |
||
| 989 | " <td>3155377.0</td>\n", |
||
| 990 | " <td>3760854</td>\n", |
||
| 991 | " <td>2658833</td>\n", |
||
| 992 | " <td>2488025</td>\n", |
||
| 993 | " <td>2506550</td>\n", |
||
| 994 | " <td>4000703</td>\n", |
||
| 995 | " <td>3292566</td>\n", |
||
| 996 | " </tr>\n", |
||
| 997 | " <tr>\n", |
||
| 998 | " <th>C00213</th>\n", |
||
| 999 | " <td>112845.0</td>\n", |
||
| 1000 | " <td>129977</td>\n", |
||
| 1001 | " <td>122292.0</td>\n", |
||
| 1002 | " <td>63219</td>\n", |
||
| 1003 | " <td>50113.0</td>\n", |
||
| 1004 | " <td>100343.0</td>\n", |
||
| 1005 | " <td>156651.0</td>\n", |
||
| 1006 | " <td>176682</td>\n", |
||
| 1007 | " <td>379322</td>\n", |
||
| 1008 | " <td>160906</td>\n", |
||
| 1009 | " <td>56802</td>\n", |
||
| 1010 | " <td>107161.0</td>\n", |
||
| 1011 | " <td>235982</td>\n", |
||
| 1012 | " <td>181200</td>\n", |
||
| 1013 | " <td>142994</td>\n", |
||
| 1014 | " <td>116132</td>\n", |
||
| 1015 | " <td>94589</td>\n", |
||
| 1016 | " <td>167280</td>\n", |
||
| 1017 | " </tr>\n", |
||
| 1018 | " </tbody>\n", |
||
| 1019 | "</table>\n", |
||
| 1020 | "</div>" |
||
| 1021 | ], |
||
| 1022 | "text/plain": [ |
||
| 1023 | " distal_M1 distal_M2 distal_M3 distal_F1 distal_F2 distal_F3 \\\n", |
||
| 1024 | "Identifier \n", |
||
| 1025 | "C00565 75170.0 57052 39170.0 84057 38608.0 64126.0 \n", |
||
| 1026 | "C00037 64511.0 33658 23565.0 52102 49508.0 37498.0 \n", |
||
| 1027 | "C01104 5787534.0 4351239 4401036.0 8187282 8431125.0 5082056.0 \n", |
||
| 1028 | "C00134 3430897.0 1877785 1225710.0 2326620 2421267.0 2595529.0 \n", |
||
| 1029 | "C00213 112845.0 129977 122292.0 63219 50113.0 100343.0 \n", |
||
| 1030 | "\n", |
||
| 1031 | " middle_M1 middle_M2 middle_M3 middle_F1 middle_F2 middle_F3 \\\n", |
||
| 1032 | "Identifier \n", |
||
| 1033 | "C00565 50214.0 75680 165178 121856 77061 98015.0 \n", |
||
| 1034 | "C00037 30417.0 55728 88519 103871 45974 73101.0 \n", |
||
| 1035 | "C01104 5138937.0 7341351 7837293 9256269 9934066 10243285.0 \n", |
||
| 1036 | "C00134 2003627.0 2120053 2269318 3220850 4596854 3155377.0 \n", |
||
| 1037 | "C00213 156651.0 176682 379322 160906 56802 107161.0 \n", |
||
| 1038 | "\n", |
||
| 1039 | " proximal_M1 proximal_M2 proximal_M3 proximal_F1 proximal_F2 \\\n", |
||
| 1040 | "Identifier \n", |
||
| 1041 | "C00565 113765 96098 84198 117644 169459 \n", |
||
| 1042 | "C00037 72725 66008 54220 95341 110192 \n", |
||
| 1043 | "C01104 7344406 5524811 4809250 9279874 9047339 \n", |
||
| 1044 | "C00134 3760854 2658833 2488025 2506550 4000703 \n", |
||
| 1045 | "C00213 235982 181200 142994 116132 94589 \n", |
||
| 1046 | "\n", |
||
| 1047 | " proximal_F3 \n", |
||
| 1048 | "Identifier \n", |
||
| 1049 | "C00565 169669 \n", |
||
| 1050 | "C00037 291598 \n", |
||
| 1051 | "C01104 9211255 \n", |
||
| 1052 | "C00134 3292566 \n", |
||
| 1053 | "C00213 167280 " |
||
| 1054 | ] |
||
| 1055 | }, |
||
| 1056 | "execution_count": 14, |
||
| 1057 | "metadata": {}, |
||
| 1058 | "output_type": "execute_result" |
||
| 1059 | } |
||
| 1060 | ], |
||
| 1061 | "source": [ |
||
| 1062 | "compound_data.head()" |
||
| 1063 | ] |
||
| 1064 | }, |
||
| 1065 | { |
||
| 1066 | "cell_type": "code", |
||
| 1067 | "execution_count": 15, |
||
| 1068 | "metadata": {}, |
||
| 1069 | "outputs": [ |
||
| 1070 | { |
||
| 1071 | "data": { |
||
| 1072 | "text/html": [ |
||
| 1073 | "<div>\n", |
||
| 1074 | "<style scoped>\n", |
||
| 1075 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 1076 | " vertical-align: middle;\n", |
||
| 1077 | " }\n", |
||
| 1078 | "\n", |
||
| 1079 | " .dataframe tbody tr th {\n", |
||
| 1080 | " vertical-align: top;\n", |
||
| 1081 | " }\n", |
||
| 1082 | "\n", |
||
| 1083 | " .dataframe thead th {\n", |
||
| 1084 | " text-align: right;\n", |
||
| 1085 | " }\n", |
||
| 1086 | "</style>\n", |
||
| 1087 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 1088 | " <thead>\n", |
||
| 1089 | " <tr style=\"text-align: right;\">\n", |
||
| 1090 | " <th></th>\n", |
||
| 1091 | " <th>group</th>\n", |
||
| 1092 | " </tr>\n", |
||
| 1093 | " <tr>\n", |
||
| 1094 | " <th>sample</th>\n", |
||
| 1095 | " <th></th>\n", |
||
| 1096 | " </tr>\n", |
||
| 1097 | " </thead>\n", |
||
| 1098 | " <tbody>\n", |
||
| 1099 | " <tr>\n", |
||
| 1100 | " <th>distal_M1</th>\n", |
||
| 1101 | " <td>Distal</td>\n", |
||
| 1102 | " </tr>\n", |
||
| 1103 | " <tr>\n", |
||
| 1104 | " <th>distal_M2</th>\n", |
||
| 1105 | " <td>Distal</td>\n", |
||
| 1106 | " </tr>\n", |
||
| 1107 | " <tr>\n", |
||
| 1108 | " <th>distal_M3</th>\n", |
||
| 1109 | " <td>Distal</td>\n", |
||
| 1110 | " </tr>\n", |
||
| 1111 | " <tr>\n", |
||
| 1112 | " <th>distal_F1</th>\n", |
||
| 1113 | " <td>Distal</td>\n", |
||
| 1114 | " </tr>\n", |
||
| 1115 | " <tr>\n", |
||
| 1116 | " <th>distal_F2</th>\n", |
||
| 1117 | " <td>Distal</td>\n", |
||
| 1118 | " </tr>\n", |
||
| 1119 | " <tr>\n", |
||
| 1120 | " <th>distal_F3</th>\n", |
||
| 1121 | " <td>Distal</td>\n", |
||
| 1122 | " </tr>\n", |
||
| 1123 | " <tr>\n", |
||
| 1124 | " <th>middle_M1</th>\n", |
||
| 1125 | " <td>Middle</td>\n", |
||
| 1126 | " </tr>\n", |
||
| 1127 | " <tr>\n", |
||
| 1128 | " <th>middle_M2</th>\n", |
||
| 1129 | " <td>Middle</td>\n", |
||
| 1130 | " </tr>\n", |
||
| 1131 | " <tr>\n", |
||
| 1132 | " <th>middle_M3</th>\n", |
||
| 1133 | " <td>Middle</td>\n", |
||
| 1134 | " </tr>\n", |
||
| 1135 | " <tr>\n", |
||
| 1136 | " <th>middle_F1</th>\n", |
||
| 1137 | " <td>Middle</td>\n", |
||
| 1138 | " </tr>\n", |
||
| 1139 | " <tr>\n", |
||
| 1140 | " <th>middle_F2</th>\n", |
||
| 1141 | " <td>Middle</td>\n", |
||
| 1142 | " </tr>\n", |
||
| 1143 | " <tr>\n", |
||
| 1144 | " <th>middle_F3</th>\n", |
||
| 1145 | " <td>Middle</td>\n", |
||
| 1146 | " </tr>\n", |
||
| 1147 | " <tr>\n", |
||
| 1148 | " <th>proximal_M1</th>\n", |
||
| 1149 | " <td>Proximal</td>\n", |
||
| 1150 | " </tr>\n", |
||
| 1151 | " <tr>\n", |
||
| 1152 | " <th>proximal_M2</th>\n", |
||
| 1153 | " <td>Proximal</td>\n", |
||
| 1154 | " </tr>\n", |
||
| 1155 | " <tr>\n", |
||
| 1156 | " <th>proximal_M3</th>\n", |
||
| 1157 | " <td>Proximal</td>\n", |
||
| 1158 | " </tr>\n", |
||
| 1159 | " <tr>\n", |
||
| 1160 | " <th>proximal_F1</th>\n", |
||
| 1161 | " <td>Proximal</td>\n", |
||
| 1162 | " </tr>\n", |
||
| 1163 | " <tr>\n", |
||
| 1164 | " <th>proximal_F2</th>\n", |
||
| 1165 | " <td>Proximal</td>\n", |
||
| 1166 | " </tr>\n", |
||
| 1167 | " <tr>\n", |
||
| 1168 | " <th>proximal_F3</th>\n", |
||
| 1169 | " <td>Proximal</td>\n", |
||
| 1170 | " </tr>\n", |
||
| 1171 | " </tbody>\n", |
||
| 1172 | "</table>\n", |
||
| 1173 | "</div>" |
||
| 1174 | ], |
||
| 1175 | "text/plain": [ |
||
| 1176 | " group\n", |
||
| 1177 | "sample \n", |
||
| 1178 | "distal_M1 Distal\n", |
||
| 1179 | "distal_M2 Distal\n", |
||
| 1180 | "distal_M3 Distal\n", |
||
| 1181 | "distal_F1 Distal\n", |
||
| 1182 | "distal_F2 Distal\n", |
||
| 1183 | "distal_F3 Distal\n", |
||
| 1184 | "middle_M1 Middle\n", |
||
| 1185 | "middle_M2 Middle\n", |
||
| 1186 | "middle_M3 Middle\n", |
||
| 1187 | "middle_F1 Middle\n", |
||
| 1188 | "middle_F2 Middle\n", |
||
| 1189 | "middle_F3 Middle\n", |
||
| 1190 | "proximal_M1 Proximal\n", |
||
| 1191 | "proximal_M2 Proximal\n", |
||
| 1192 | "proximal_M3 Proximal\n", |
||
| 1193 | "proximal_F1 Proximal\n", |
||
| 1194 | "proximal_F2 Proximal\n", |
||
| 1195 | "proximal_F3 Proximal" |
||
| 1196 | ] |
||
| 1197 | }, |
||
| 1198 | "execution_count": 15, |
||
| 1199 | "metadata": {}, |
||
| 1200 | "output_type": "execute_result" |
||
| 1201 | } |
||
| 1202 | ], |
||
| 1203 | "source": [ |
||
| 1204 | "compound_design" |
||
| 1205 | ] |
||
| 1206 | }, |
||
| 1207 | { |
||
| 1208 | "cell_type": "code", |
||
| 1209 | "execution_count": 16, |
||
| 1210 | "metadata": {}, |
||
| 1211 | "outputs": [ |
||
| 1212 | { |
||
| 1213 | "data": { |
||
| 1214 | "text/plain": [ |
||
| 1215 | "1" |
||
| 1216 | ] |
||
| 1217 | }, |
||
| 1218 | "execution_count": 16, |
||
| 1219 | "metadata": {}, |
||
| 1220 | "output_type": "execute_result" |
||
| 1221 | } |
||
| 1222 | ], |
||
| 1223 | "source": [ |
||
| 1224 | "set_log_level_info()" |
||
| 1225 | ] |
||
| 1226 | }, |
||
| 1227 | { |
||
| 1228 | "cell_type": "markdown", |
||
| 1229 | "metadata": {}, |
||
| 1230 | "source": [ |
||
| 1231 | "## Create omics data" |
||
| 1232 | ] |
||
| 1233 | }, |
||
| 1234 | { |
||
| 1235 | "cell_type": "code", |
||
| 1236 | "execution_count": 17, |
||
| 1237 | "metadata": {}, |
||
| 1238 | "outputs": [ |
||
| 1239 | { |
||
| 1240 | "data": { |
||
| 1241 | "text/plain": [ |
||
| 1242 | "genes data with (31953, 15) measurements" |
||
| 1243 | ] |
||
| 1244 | }, |
||
| 1245 | "execution_count": 17, |
||
| 1246 | "metadata": {}, |
||
| 1247 | "output_type": "execute_result" |
||
| 1248 | } |
||
| 1249 | ], |
||
| 1250 | "source": [ |
||
| 1251 | "transcript_data = SingleOmicsData(GENES, gene_data, gene_design)\n", |
||
| 1252 | "transcript_data" |
||
| 1253 | ] |
||
| 1254 | }, |
||
| 1255 | { |
||
| 1256 | "cell_type": "code", |
||
| 1257 | "execution_count": 18, |
||
| 1258 | "metadata": {}, |
||
| 1259 | "outputs": [ |
||
| 1260 | { |
||
| 1261 | "data": { |
||
| 1262 | "text/plain": [ |
||
| 1263 | "proteins data with (3061, 12) measurements" |
||
| 1264 | ] |
||
| 1265 | }, |
||
| 1266 | "execution_count": 18, |
||
| 1267 | "metadata": {}, |
||
| 1268 | "output_type": "execute_result" |
||
| 1269 | } |
||
| 1270 | ], |
||
| 1271 | "source": [ |
||
| 1272 | "protein_data = SingleOmicsData(PROTEINS, protein_data, protein_design)\n", |
||
| 1273 | "protein_data" |
||
| 1274 | ] |
||
| 1275 | }, |
||
| 1276 | { |
||
| 1277 | "cell_type": "code", |
||
| 1278 | "execution_count": 19, |
||
| 1279 | "metadata": {}, |
||
| 1280 | "outputs": [ |
||
| 1281 | { |
||
| 1282 | "data": { |
||
| 1283 | "text/plain": [ |
||
| 1284 | "compounds data with (130, 18) measurements" |
||
| 1285 | ] |
||
| 1286 | }, |
||
| 1287 | "execution_count": 19, |
||
| 1288 | "metadata": {}, |
||
| 1289 | "output_type": "execute_result" |
||
| 1290 | } |
||
| 1291 | ], |
||
| 1292 | "source": [ |
||
| 1293 | "compound_data = SingleOmicsData(COMPOUNDS, compound_data, compound_design)\n", |
||
| 1294 | "compound_data" |
||
| 1295 | ] |
||
| 1296 | }, |
||
| 1297 | { |
||
| 1298 | "cell_type": "code", |
||
| 1299 | "execution_count": 20, |
||
| 1300 | "metadata": {}, |
||
| 1301 | "outputs": [], |
||
| 1302 | "source": [ |
||
| 1303 | "publication = 'Rabinowitz, Jeremy S., et al. \"Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish.\" Proceedings of the National Academy of Sciences 114.5 (2017): E717-E726.'\n", |
||
| 1304 | "url = 'https://www.pnas.org/content/114/5/E717.short'" |
||
| 1305 | ] |
||
| 1306 | }, |
||
| 1307 | { |
||
| 1308 | "cell_type": "code", |
||
| 1309 | "execution_count": 21, |
||
| 1310 | "metadata": {}, |
||
| 1311 | "outputs": [ |
||
| 1312 | { |
||
| 1313 | "data": { |
||
| 1314 | "text/plain": [ |
||
| 1315 | "Multi-omics data container\n", |
||
| 1316 | "- publication: Rabinowitz, Jeremy S., et al. \"Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish.\" Proceedings of the National Academy of Sciences 114.5 (2017): E717-E726.\n", |
||
| 1317 | "- URL: https://www.pnas.org/content/114/5/E717.short\n", |
||
| 1318 | "- Views: 3 modalities\n", |
||
| 1319 | "\t - genes data with (31953, 15) measurements\n", |
||
| 1320 | "\t - proteins data with (3061, 12) measurements\n", |
||
| 1321 | "\t - compounds data with (130, 18) measurements" |
||
| 1322 | ] |
||
| 1323 | }, |
||
| 1324 | "execution_count": 21, |
||
| 1325 | "metadata": {}, |
||
| 1326 | "output_type": "execute_result" |
||
| 1327 | } |
||
| 1328 | ], |
||
| 1329 | "source": [ |
||
| 1330 | "mo = MultiOmicsData(publication=publication, url=url)\n", |
||
| 1331 | "mo.add_data([transcript_data, protein_data, compound_data])\n", |
||
| 1332 | "mo" |
||
| 1333 | ] |
||
| 1334 | }, |
||
| 1335 | { |
||
| 1336 | "cell_type": "markdown", |
||
| 1337 | "metadata": {}, |
||
| 1338 | "source": [ |
||
| 1339 | "## Create a mapping object" |
||
| 1340 | ] |
||
| 1341 | }, |
||
| 1342 | { |
||
| 1343 | "cell_type": "markdown", |
||
| 1344 | "metadata": {}, |
||
| 1345 | "source": [ |
||
| 1346 | "The mapping object uses Reactome to map the different biological entities in the data:\n", |
||
| 1347 | "- Transcripts (or genes) are connected to the proteins they encode\n", |
||
| 1348 | "- Proteins and compounds are connected to reactions they're involved in\n", |
||
| 1349 | "- Reactions are connected to pathways" |
||
| 1350 | ] |
||
| 1351 | }, |
||
| 1352 | { |
||
| 1353 | "cell_type": "code", |
||
| 1354 | "execution_count": 22, |
||
| 1355 | "metadata": {}, |
||
| 1356 | "outputs": [ |
||
| 1357 | { |
||
| 1358 | "name": "stderr", |
||
| 1359 | "output_type": "stream", |
||
| 1360 | "text": [ |
||
| 1361 | "2022-03-24 14:40:26.569 | INFO | pyMultiOmics.functions:remove_dupes:385 - Removing 2 rows with duplicate identifiers\n", |
||
| 1362 | "2022-03-24 14:40:26.570 | INFO | pyMultiOmics.functions:reactome_mapping:78 - There are 128 observed compound ids\n", |
||
| 1363 | "2022-03-24 14:40:26.571 | INFO | pyMultiOmics.functions:reactome_mapping:81 - Mapping genes -> proteins\n", |
||
| 1364 | "2022-03-24 14:40:34.971 | INFO | pyMultiOmics.functions:reactome_mapping:86 - Mapping proteins -> reactions\n", |
||
| 1365 | "2022-03-24 14:40:46.041 | INFO | pyMultiOmics.functions:reactome_mapping:94 - Mapping compounds -> reactions\n", |
||
| 1366 | "2022-03-24 14:40:49.516 | INFO | pyMultiOmics.functions:reactome_mapping:100 - Mapping reactions -> pathways\n", |
||
| 1367 | "2022-03-24 14:40:50.558 | INFO | pyMultiOmics.functions:reactome_mapping:111 - Mapping reactions -> proteins\n", |
||
| 1368 | "2022-03-24 14:40:57.492 | INFO | pyMultiOmics.functions:reactome_mapping:118 - Mapping reactions -> compounds\n", |
||
| 1369 | "2022-03-24 14:41:01.232 | INFO | pyMultiOmics.functions:reactome_mapping:130 - Mapping proteins -> genes\n", |
||
| 1370 | "2022-03-24 14:41:18.641 | INFO | pyMultiOmics.mapping:_add_nodes:153 - Processing nodes: genes\n", |
||
| 1371 | "2022-03-24 14:41:19.903 | INFO | pyMultiOmics.mapping:_add_nodes:153 - Processing nodes: proteins\n", |
||
| 1372 | "2022-03-24 14:41:20.231 | INFO | pyMultiOmics.mapping:_add_nodes:153 - Processing nodes: compounds\n", |
||
| 1373 | "2022-03-24 14:41:20.289 | INFO | pyMultiOmics.mapping:_add_nodes:153 - Processing nodes: reactions\n", |
||
| 1374 | "2022-03-24 14:41:20.463 | INFO | pyMultiOmics.mapping:_add_nodes:153 - Processing nodes: pathways\n", |
||
| 1375 | "2022-03-24 14:41:20.470 | INFO | pyMultiOmics.mapping:_add_edges:201 - Processing edges: gene_proteins\n", |
||
| 1376 | "2022-03-24 14:41:20.647 | INFO | pyMultiOmics.mapping:_add_edges:201 - Processing edges: protein_reactions\n", |
||
| 1377 | "2022-03-24 14:41:21.793 | INFO | pyMultiOmics.mapping:_add_edges:201 - Processing edges: compound_reactions\n", |
||
| 1378 | "2022-03-24 14:41:22.134 | INFO | pyMultiOmics.mapping:_add_edges:201 - Processing edges: reaction_pathways\n", |
||
| 1379 | "2022-03-24 14:41:22.366 | INFO | pyMultiOmics.mapping:build:51 - Created a multi-omics network with 21264 nodes and 22682 edges\n", |
||
| 1380 | "2022-03-24 14:41:22.385 | INFO | pyMultiOmics.mapping:build:53 - node_counts = {'genes': 9371, 'proteins': 8221, 'compounds': 1794, 'reactions': 1629, 'pathways': 249}\n" |
||
| 1381 | ] |
||
| 1382 | }, |
||
| 1383 | { |
||
| 1384 | "data": { |
||
| 1385 | "text/plain": [ |
||
| 1386 | "<pyMultiOmics.mapping.Mapper at 0x174b0a440>" |
||
| 1387 | ] |
||
| 1388 | }, |
||
| 1389 | "execution_count": 22, |
||
| 1390 | "metadata": {}, |
||
| 1391 | "output_type": "execute_result" |
||
| 1392 | } |
||
| 1393 | ], |
||
| 1394 | "source": [ |
||
| 1395 | "m = Mapper(mo, DANIO_RERIO, metabolic_pathway_only=True)\n", |
||
| 1396 | "m.build()" |
||
| 1397 | ] |
||
| 1398 | }, |
||
| 1399 | { |
||
| 1400 | "cell_type": "code", |
||
| 1401 | "execution_count": 23, |
||
| 1402 | "metadata": {}, |
||
| 1403 | "outputs": [ |
||
| 1404 | { |
||
| 1405 | "data": { |
||
| 1406 | "text/plain": [ |
||
| 1407 | "<pyMultiOmics.mapping.Mapper at 0x174b0a440>" |
||
| 1408 | ] |
||
| 1409 | }, |
||
| 1410 | "execution_count": 23, |
||
| 1411 | "metadata": {}, |
||
| 1412 | "output_type": "execute_result" |
||
| 1413 | } |
||
| 1414 | ], |
||
| 1415 | "source": [ |
||
| 1416 | "m" |
||
| 1417 | ] |
||
| 1418 | }, |
||
| 1419 | { |
||
| 1420 | "cell_type": "markdown", |
||
| 1421 | "metadata": {}, |
||
| 1422 | "source": [ |
||
| 1423 | "## Querying mapping object" |
||
| 1424 | ] |
||
| 1425 | }, |
||
| 1426 | { |
||
| 1427 | "cell_type": "markdown", |
||
| 1428 | "metadata": {}, |
||
| 1429 | "source": [ |
||
| 1430 | "Below shows some example queries we can perform with the mapping object" |
||
| 1431 | ] |
||
| 1432 | }, |
||
| 1433 | { |
||
| 1434 | "cell_type": "markdown", |
||
| 1435 | "metadata": {}, |
||
| 1436 | "source": [ |
||
| 1437 | "##### Find reactions that are connected to some observed genes, proteins and compounds in the data" |
||
| 1438 | ] |
||
| 1439 | }, |
||
| 1440 | { |
||
| 1441 | "cell_type": "code", |
||
| 1442 | "execution_count": 24, |
||
| 1443 | "metadata": {}, |
||
| 1444 | "outputs": [ |
||
| 1445 | { |
||
| 1446 | "data": { |
||
| 1447 | "text/html": [ |
||
| 1448 | "<div>\n", |
||
| 1449 | "<style scoped>\n", |
||
| 1450 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 1451 | " vertical-align: middle;\n", |
||
| 1452 | " }\n", |
||
| 1453 | "\n", |
||
| 1454 | " .dataframe tbody tr th {\n", |
||
| 1455 | " vertical-align: top;\n", |
||
| 1456 | " }\n", |
||
| 1457 | "\n", |
||
| 1458 | " .dataframe thead th {\n", |
||
| 1459 | " text-align: right;\n", |
||
| 1460 | " }\n", |
||
| 1461 | "</style>\n", |
||
| 1462 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 1463 | " <thead>\n", |
||
| 1464 | " <tr style=\"text-align: right;\">\n", |
||
| 1465 | " <th></th>\n", |
||
| 1466 | " <th>reaction_id</th>\n", |
||
| 1467 | " <th>reaction_name</th>\n", |
||
| 1468 | " <th>num_genes</th>\n", |
||
| 1469 | " <th>num_proteins</th>\n", |
||
| 1470 | " <th>num_compounds</th>\n", |
||
| 1471 | " </tr>\n", |
||
| 1472 | " </thead>\n", |
||
| 1473 | " <tbody>\n", |
||
| 1474 | " <tr>\n", |
||
| 1475 | " <th>0</th>\n", |
||
| 1476 | " <td>R-DRE-109278</td>\n", |
||
| 1477 | " <td>Nt5e:zn2+ hydrolyses amp,damp,gmp, imp</td>\n", |
||
| 1478 | " <td>1</td>\n", |
||
| 1479 | " <td>1</td>\n", |
||
| 1480 | " <td>3</td>\n", |
||
| 1481 | " </tr>\n", |
||
| 1482 | " <tr>\n", |
||
| 1483 | " <th>1</th>\n", |
||
| 1484 | " <td>R-DRE-109291</td>\n", |
||
| 1485 | " <td>Cmp or tmp or ump + h2o => cytidine, thymidine...</td>\n", |
||
| 1486 | " <td>1</td>\n", |
||
| 1487 | " <td>1</td>\n", |
||
| 1488 | " <td>2</td>\n", |
||
| 1489 | " </tr>\n", |
||
| 1490 | " <tr>\n", |
||
| 1491 | " <th>2</th>\n", |
||
| 1492 | " <td>R-DRE-109415</td>\n", |
||
| 1493 | " <td>Amp + h2o => adenosine + orthophosphate [nt5c1b]</td>\n", |
||
| 1494 | " <td>1</td>\n", |
||
| 1495 | " <td>1</td>\n", |
||
| 1496 | " <td>1</td>\n", |
||
| 1497 | " </tr>\n", |
||
| 1498 | " <tr>\n", |
||
| 1499 | " <th>3</th>\n", |
||
| 1500 | " <td>R-DRE-109624</td>\n", |
||
| 1501 | " <td>(2-deoxy)adenosine + atp => (d)amp + adp (adk)</td>\n", |
||
| 1502 | " <td>1</td>\n", |
||
| 1503 | " <td>1</td>\n", |
||
| 1504 | " <td>1</td>\n", |
||
| 1505 | " </tr>\n", |
||
| 1506 | " <tr>\n", |
||
| 1507 | " <th>4</th>\n", |
||
| 1508 | " <td>R-DRE-1237160</td>\n", |
||
| 1509 | " <td>Mta is cleaved and phosphorylated</td>\n", |
||
| 1510 | " <td>1</td>\n", |
||
| 1511 | " <td>1</td>\n", |
||
| 1512 | " <td>1</td>\n", |
||
| 1513 | " </tr>\n", |
||
| 1514 | " <tr>\n", |
||
| 1515 | " <th>5</th>\n", |
||
| 1516 | " <td>R-DRE-1247910</td>\n", |
||
| 1517 | " <td>Cndp2:2mn2+ dimer hydrolyses cysgly</td>\n", |
||
| 1518 | " <td>1</td>\n", |
||
| 1519 | " <td>1</td>\n", |
||
| 1520 | " <td>1</td>\n", |
||
| 1521 | " </tr>\n", |
||
| 1522 | " <tr>\n", |
||
| 1523 | " <th>6</th>\n", |
||
| 1524 | " <td>R-DRE-139970</td>\n", |
||
| 1525 | " <td>Fmo3:fad n-oxidises tma to tmao</td>\n", |
||
| 1526 | " <td>3</td>\n", |
||
| 1527 | " <td>1</td>\n", |
||
| 1528 | " <td>2</td>\n", |
||
| 1529 | " </tr>\n", |
||
| 1530 | " <tr>\n", |
||
| 1531 | " <th>7</th>\n", |
||
| 1532 | " <td>R-DRE-1482976</td>\n", |
||
| 1533 | " <td>Cdp-dag is converted to pi by cdipt</td>\n", |
||
| 1534 | " <td>1</td>\n", |
||
| 1535 | " <td>1</td>\n", |
||
| 1536 | " <td>1</td>\n", |
||
| 1537 | " </tr>\n", |
||
| 1538 | " <tr>\n", |
||
| 1539 | " <th>8</th>\n", |
||
| 1540 | " <td>R-DRE-1614583</td>\n", |
||
| 1541 | " <td>Pxlp-k212-cth cleaves l-cystathionine</td>\n", |
||
| 1542 | " <td>1</td>\n", |
||
| 1543 | " <td>1</td>\n", |
||
| 1544 | " <td>1</td>\n", |
||
| 1545 | " </tr>\n", |
||
| 1546 | " <tr>\n", |
||
| 1547 | " <th>9</th>\n", |
||
| 1548 | " <td>R-DRE-174401</td>\n", |
||
| 1549 | " <td>Ahcy:nad+ tetramer hydrolyses adohcy</td>\n", |
||
| 1550 | " <td>1</td>\n", |
||
| 1551 | " <td>1</td>\n", |
||
| 1552 | " <td>1</td>\n", |
||
| 1553 | " </tr>\n", |
||
| 1554 | " <tr>\n", |
||
| 1555 | " <th>10</th>\n", |
||
| 1556 | " <td>R-DRE-1855154</td>\n", |
||
| 1557 | " <td>I1p is dephosphorylated to ins by impa1/2 in t...</td>\n", |
||
| 1558 | " <td>2</td>\n", |
||
| 1559 | " <td>1</td>\n", |
||
| 1560 | " <td>1</td>\n", |
||
| 1561 | " </tr>\n", |
||
| 1562 | " <tr>\n", |
||
| 1563 | " <th>11</th>\n", |
||
| 1564 | " <td>R-DRE-1855210</td>\n", |
||
| 1565 | " <td>I3p is dephosphorylated to ins by impa1/2 in t...</td>\n", |
||
| 1566 | " <td>2</td>\n", |
||
| 1567 | " <td>1</td>\n", |
||
| 1568 | " <td>1</td>\n", |
||
| 1569 | " </tr>\n", |
||
| 1570 | " <tr>\n", |
||
| 1571 | " <th>12</th>\n", |
||
| 1572 | " <td>R-DRE-1855211</td>\n", |
||
| 1573 | " <td>I4p is dephosphorylated to ins by impa1/2 in t...</td>\n", |
||
| 1574 | " <td>2</td>\n", |
||
| 1575 | " <td>1</td>\n", |
||
| 1576 | " <td>1</td>\n", |
||
| 1577 | " </tr>\n", |
||
| 1578 | " <tr>\n", |
||
| 1579 | " <th>13</th>\n", |
||
| 1580 | " <td>R-DRE-188467</td>\n", |
||
| 1581 | " <td>Gly-3-p+fad->dhap+fadh2 (catalyzed by mitochon...</td>\n", |
||
| 1582 | " <td>1</td>\n", |
||
| 1583 | " <td>1</td>\n", |
||
| 1584 | " <td>1</td>\n", |
||
| 1585 | " </tr>\n", |
||
| 1586 | " <tr>\n", |
||
| 1587 | " <th>14</th>\n", |
||
| 1588 | " <td>R-DRE-197250</td>\n", |
||
| 1589 | " <td>Nampt transfers prib to nam to form namn</td>\n", |
||
| 1590 | " <td>1</td>\n", |
||
| 1591 | " <td>1</td>\n", |
||
| 1592 | " <td>1</td>\n", |
||
| 1593 | " </tr>\n", |
||
| 1594 | " <tr>\n", |
||
| 1595 | " <th>15</th>\n", |
||
| 1596 | " <td>R-DRE-198813</td>\n", |
||
| 1597 | " <td>Gsto dimers reduce deha to asch-</td>\n", |
||
| 1598 | " <td>2</td>\n", |
||
| 1599 | " <td>2</td>\n", |
||
| 1600 | " <td>1</td>\n", |
||
| 1601 | " </tr>\n", |
||
| 1602 | " <tr>\n", |
||
| 1603 | " <th>16</th>\n", |
||
| 1604 | " <td>R-DRE-200318</td>\n", |
||
| 1605 | " <td>Creatine + atp => phosphocreatine + adp [ckb,ckm]</td>\n", |
||
| 1606 | " <td>2</td>\n", |
||
| 1607 | " <td>2</td>\n", |
||
| 1608 | " <td>1</td>\n", |
||
| 1609 | " </tr>\n", |
||
| 1610 | " <tr>\n", |
||
| 1611 | " <th>17</th>\n", |
||
| 1612 | " <td>R-DRE-200326</td>\n", |
||
| 1613 | " <td>Creatine + atp => phosphocreatine + adp [ck oc...</td>\n", |
||
| 1614 | " <td>1</td>\n", |
||
| 1615 | " <td>1</td>\n", |
||
| 1616 | " <td>1</td>\n", |
||
| 1617 | " </tr>\n", |
||
| 1618 | " <tr>\n", |
||
| 1619 | " <th>18</th>\n", |
||
| 1620 | " <td>R-DRE-202127</td>\n", |
||
| 1621 | " <td>Enos synthesizes no</td>\n", |
||
| 1622 | " <td>4</td>\n", |
||
| 1623 | " <td>2</td>\n", |
||
| 1624 | " <td>1</td>\n", |
||
| 1625 | " </tr>\n", |
||
| 1626 | " <tr>\n", |
||
| 1627 | " <th>19</th>\n", |
||
| 1628 | " <td>R-DRE-2162066</td>\n", |
||
| 1629 | " <td>Carbovir + imp => carbovir monophosphate + ino...</td>\n", |
||
| 1630 | " <td>1</td>\n", |
||
| 1631 | " <td>1</td>\n", |
||
| 1632 | " <td>1</td>\n", |
||
| 1633 | " </tr>\n", |
||
| 1634 | " <tr>\n", |
||
| 1635 | " <th>20</th>\n", |
||
| 1636 | " <td>R-DRE-2993447</td>\n", |
||
| 1637 | " <td>Hlcs biotinylates 6x(pcca:pccb)</td>\n", |
||
| 1638 | " <td>3</td>\n", |
||
| 1639 | " <td>1</td>\n", |
||
| 1640 | " <td>1</td>\n", |
||
| 1641 | " </tr>\n", |
||
| 1642 | " <tr>\n", |
||
| 1643 | " <th>21</th>\n", |
||
| 1644 | " <td>R-DRE-2993799</td>\n", |
||
| 1645 | " <td>Hlcs biotinylates 6xmccc1:6xmccc2</td>\n", |
||
| 1646 | " <td>3</td>\n", |
||
| 1647 | " <td>1</td>\n", |
||
| 1648 | " <td>1</td>\n", |
||
| 1649 | " </tr>\n", |
||
| 1650 | " <tr>\n", |
||
| 1651 | " <th>22</th>\n", |
||
| 1652 | " <td>R-DRE-3301943</td>\n", |
||
| 1653 | " <td>Gstk1 dimer transfers gs from gsh to cdnb</td>\n", |
||
| 1654 | " <td>1</td>\n", |
||
| 1655 | " <td>1</td>\n", |
||
| 1656 | " <td>1</td>\n", |
||
| 1657 | " </tr>\n", |
||
| 1658 | " <tr>\n", |
||
| 1659 | " <th>23</th>\n", |
||
| 1660 | " <td>R-DRE-350604</td>\n", |
||
| 1661 | " <td>Agmatine + h2o <=> putrescine + urea</td>\n", |
||
| 1662 | " <td>1</td>\n", |
||
| 1663 | " <td>1</td>\n", |
||
| 1664 | " <td>1</td>\n", |
||
| 1665 | " </tr>\n", |
||
| 1666 | " <tr>\n", |
||
| 1667 | " <th>24</th>\n", |
||
| 1668 | " <td>R-DRE-351215</td>\n", |
||
| 1669 | " <td>Putrescine + dc-adenosyl methionine => spermi...</td>\n", |
||
| 1670 | " <td>1</td>\n", |
||
| 1671 | " <td>1</td>\n", |
||
| 1672 | " <td>2</td>\n", |
||
| 1673 | " </tr>\n", |
||
| 1674 | " <tr>\n", |
||
| 1675 | " <th>25</th>\n", |
||
| 1676 | " <td>R-DRE-372519</td>\n", |
||
| 1677 | " <td>Accho is hydrolyzed to cho and acetate by ache</td>\n", |
||
| 1678 | " <td>2</td>\n", |
||
| 1679 | " <td>2</td>\n", |
||
| 1680 | " <td>2</td>\n", |
||
| 1681 | " </tr>\n", |
||
| 1682 | " <tr>\n", |
||
| 1683 | " <th>26</th>\n", |
||
| 1684 | " <td>R-DRE-372819</td>\n", |
||
| 1685 | " <td>Oxaloacetate + gtp => phosphoenolpyruvate + gd...</td>\n", |
||
| 1686 | " <td>1</td>\n", |
||
| 1687 | " <td>1</td>\n", |
||
| 1688 | " <td>1</td>\n", |
||
| 1689 | " </tr>\n", |
||
| 1690 | " <tr>\n", |
||
| 1691 | " <th>27</th>\n", |
||
| 1692 | " <td>R-DRE-416530</td>\n", |
||
| 1693 | " <td>Ffar1:ffar1 ligands activates gq</td>\n", |
||
| 1694 | " <td>5</td>\n", |
||
| 1695 | " <td>1</td>\n", |
||
| 1696 | " <td>1</td>\n", |
||
| 1697 | " </tr>\n", |
||
| 1698 | " <tr>\n", |
||
| 1699 | " <th>28</th>\n", |
||
| 1700 | " <td>R-DRE-5652172</td>\n", |
||
| 1701 | " <td>Akr1b1 reduces glc to d-sorbitol</td>\n", |
||
| 1702 | " <td>2</td>\n", |
||
| 1703 | " <td>1</td>\n", |
||
| 1704 | " <td>1</td>\n", |
||
| 1705 | " </tr>\n", |
||
| 1706 | " <tr>\n", |
||
| 1707 | " <th>29</th>\n", |
||
| 1708 | " <td>R-DRE-5693373</td>\n", |
||
| 1709 | " <td>Ddah1,2 hydrolyses adma to dma and l-cit</td>\n", |
||
| 1710 | " <td>1</td>\n", |
||
| 1711 | " <td>1</td>\n", |
||
| 1712 | " <td>1</td>\n", |
||
| 1713 | " </tr>\n", |
||
| 1714 | " <tr>\n", |
||
| 1715 | " <th>30</th>\n", |
||
| 1716 | " <td>R-DRE-5693724</td>\n", |
||
| 1717 | " <td>Esd dimer hydrolyses s-fgsh to gsh</td>\n", |
||
| 1718 | " <td>1</td>\n", |
||
| 1719 | " <td>1</td>\n", |
||
| 1720 | " <td>1</td>\n", |
||
| 1721 | " </tr>\n", |
||
| 1722 | " <tr>\n", |
||
| 1723 | " <th>31</th>\n", |
||
| 1724 | " <td>R-DRE-6783221</td>\n", |
||
| 1725 | " <td>Hagh hydrolyses (r)-s-lgsh to gsh and lact</td>\n", |
||
| 1726 | " <td>1</td>\n", |
||
| 1727 | " <td>1</td>\n", |
||
| 1728 | " <td>1</td>\n", |
||
| 1729 | " </tr>\n", |
||
| 1730 | " <tr>\n", |
||
| 1731 | " <th>32</th>\n", |
||
| 1732 | " <td>R-DRE-6783880</td>\n", |
||
| 1733 | " <td>Pipox oxidises ppca to p6c</td>\n", |
||
| 1734 | " <td>1</td>\n", |
||
| 1735 | " <td>1</td>\n", |
||
| 1736 | " <td>1</td>\n", |
||
| 1737 | " </tr>\n", |
||
| 1738 | " <tr>\n", |
||
| 1739 | " <th>33</th>\n", |
||
| 1740 | " <td>R-DRE-6784393</td>\n", |
||
| 1741 | " <td>Pxlp-k279-got2 dimer transaminates 4-oh-l-glut...</td>\n", |
||
| 1742 | " <td>2</td>\n", |
||
| 1743 | " <td>2</td>\n", |
||
| 1744 | " <td>1</td>\n", |
||
| 1745 | " </tr>\n", |
||
| 1746 | " <tr>\n", |
||
| 1747 | " <th>34</th>\n", |
||
| 1748 | " <td>R-DRE-6797653</td>\n", |
||
| 1749 | " <td>Dmgdh:fad oxidatively demethylates dmgly to sarc</td>\n", |
||
| 1750 | " <td>1</td>\n", |
||
| 1751 | " <td>1</td>\n", |
||
| 1752 | " <td>2</td>\n", |
||
| 1753 | " </tr>\n", |
||
| 1754 | " <tr>\n", |
||
| 1755 | " <th>35</th>\n", |
||
| 1756 | " <td>R-DRE-6797955</td>\n", |
||
| 1757 | " <td>Aldh7a1 oxidises betald to bet</td>\n", |
||
| 1758 | " <td>1</td>\n", |
||
| 1759 | " <td>1</td>\n", |
||
| 1760 | " <td>1</td>\n", |
||
| 1761 | " </tr>\n", |
||
| 1762 | " <tr>\n", |
||
| 1763 | " <th>36</th>\n", |
||
| 1764 | " <td>R-DRE-6798317</td>\n", |
||
| 1765 | " <td>Gnmt tetramer transfers methyl group from adom...</td>\n", |
||
| 1766 | " <td>1</td>\n", |
||
| 1767 | " <td>1</td>\n", |
||
| 1768 | " <td>1</td>\n", |
||
| 1769 | " </tr>\n", |
||
| 1770 | " <tr>\n", |
||
| 1771 | " <th>37</th>\n", |
||
| 1772 | " <td>R-DRE-6807826</td>\n", |
||
| 1773 | " <td>Ldhal6b reduces pyr to lact</td>\n", |
||
| 1774 | " <td>1</td>\n", |
||
| 1775 | " <td>1</td>\n", |
||
| 1776 | " <td>1</td>\n", |
||
| 1777 | " </tr>\n", |
||
| 1778 | " <tr>\n", |
||
| 1779 | " <th>38</th>\n", |
||
| 1780 | " <td>R-DRE-70342</td>\n", |
||
| 1781 | " <td>Aldob tetramer cleaves fru-1-p to ga and dhap</td>\n", |
||
| 1782 | " <td>1</td>\n", |
||
| 1783 | " <td>1</td>\n", |
||
| 1784 | " <td>1</td>\n", |
||
| 1785 | " </tr>\n", |
||
| 1786 | " <tr>\n", |
||
| 1787 | " <th>39</th>\n", |
||
| 1788 | " <td>R-DRE-70349</td>\n", |
||
| 1789 | " <td>Dak dimer phosphorylates d-glyceraldehyde to f...</td>\n", |
||
| 1790 | " <td>1</td>\n", |
||
| 1791 | " <td>1</td>\n", |
||
| 1792 | " <td>1</td>\n", |
||
| 1793 | " </tr>\n", |
||
| 1794 | " <tr>\n", |
||
| 1795 | " <th>40</th>\n", |
||
| 1796 | " <td>R-DRE-70510</td>\n", |
||
| 1797 | " <td>Ldh tetramer oxidises lact to pyr</td>\n", |
||
| 1798 | " <td>2</td>\n", |
||
| 1799 | " <td>2</td>\n", |
||
| 1800 | " <td>1</td>\n", |
||
| 1801 | " </tr>\n", |
||
| 1802 | " <tr>\n", |
||
| 1803 | " <th>41</th>\n", |
||
| 1804 | " <td>R-DRE-70573</td>\n", |
||
| 1805 | " <td>Argininosuccinate <=> fumarate + arginine</td>\n", |
||
| 1806 | " <td>1</td>\n", |
||
| 1807 | " <td>1</td>\n", |
||
| 1808 | " <td>1</td>\n", |
||
| 1809 | " </tr>\n", |
||
| 1810 | " <tr>\n", |
||
| 1811 | " <th>42</th>\n", |
||
| 1812 | " <td>R-DRE-70596</td>\n", |
||
| 1813 | " <td>Got2 dimer deaminates l-asp</td>\n", |
||
| 1814 | " <td>2</td>\n", |
||
| 1815 | " <td>2</td>\n", |
||
| 1816 | " <td>1</td>\n", |
||
| 1817 | " </tr>\n", |
||
| 1818 | " <tr>\n", |
||
| 1819 | " <th>43</th>\n", |
||
| 1820 | " <td>R-DRE-70613</td>\n", |
||
| 1821 | " <td>Oxaloacetate + glutamate <=> aspartate + alpha...</td>\n", |
||
| 1822 | " <td>2</td>\n", |
||
| 1823 | " <td>2</td>\n", |
||
| 1824 | " <td>1</td>\n", |
||
| 1825 | " </tr>\n", |
||
| 1826 | " <tr>\n", |
||
| 1827 | " <th>44</th>\n", |
||
| 1828 | " <td>R-DRE-70979</td>\n", |
||
| 1829 | " <td>(s)-malate + nad+ <=> oxaloacetate + nadh + h+</td>\n", |
||
| 1830 | " <td>1</td>\n", |
||
| 1831 | " <td>1</td>\n", |
||
| 1832 | " <td>1</td>\n", |
||
| 1833 | " </tr>\n", |
||
| 1834 | " <tr>\n", |
||
| 1835 | " <th>45</th>\n", |
||
| 1836 | " <td>R-DRE-71163</td>\n", |
||
| 1837 | " <td>P-hydroxyphenylpyruvate + o2 => homogentisate ...</td>\n", |
||
| 1838 | " <td>1</td>\n", |
||
| 1839 | " <td>1</td>\n", |
||
| 1840 | " <td>1</td>\n", |
||
| 1841 | " </tr>\n", |
||
| 1842 | " <tr>\n", |
||
| 1843 | " <th>46</th>\n", |
||
| 1844 | " <td>R-DRE-71260</td>\n", |
||
| 1845 | " <td>Aldh9a1 tetramer dehydrogenates teabl to form ...</td>\n", |
||
| 1846 | " <td>1</td>\n", |
||
| 1847 | " <td>1</td>\n", |
||
| 1848 | " <td>1</td>\n", |
||
| 1849 | " </tr>\n", |
||
| 1850 | " <tr>\n", |
||
| 1851 | " <th>47</th>\n", |
||
| 1852 | " <td>R-DRE-71783</td>\n", |
||
| 1853 | " <td>Oxaloacetate + nadh + h+ <=> (s)-malate + nad+</td>\n", |
||
| 1854 | " <td>1</td>\n", |
||
| 1855 | " <td>1</td>\n", |
||
| 1856 | " <td>1</td>\n", |
||
| 1857 | " </tr>\n", |
||
| 1858 | " <tr>\n", |
||
| 1859 | " <th>48</th>\n", |
||
| 1860 | " <td>R-DRE-71849</td>\n", |
||
| 1861 | " <td>Ldh tetramer reduces pyr to lact</td>\n", |
||
| 1862 | " <td>2</td>\n", |
||
| 1863 | " <td>2</td>\n", |
||
| 1864 | " <td>1</td>\n", |
||
| 1865 | " </tr>\n", |
||
| 1866 | " <tr>\n", |
||
| 1867 | " <th>49</th>\n", |
||
| 1868 | " <td>R-DRE-74241</td>\n", |
||
| 1869 | " <td>Ada catalyzes the deamination of (deoxy)adenosine</td>\n", |
||
| 1870 | " <td>1</td>\n", |
||
| 1871 | " <td>1</td>\n", |
||
| 1872 | " <td>2</td>\n", |
||
| 1873 | " </tr>\n", |
||
| 1874 | " <tr>\n", |
||
| 1875 | " <th>50</th>\n", |
||
| 1876 | " <td>R-DRE-74248</td>\n", |
||
| 1877 | " <td>(d)gmp or (d)imp + h2o => (2-deoxy)guanosine o...</td>\n", |
||
| 1878 | " <td>1</td>\n", |
||
| 1879 | " <td>1</td>\n", |
||
| 1880 | " <td>2</td>\n", |
||
| 1881 | " </tr>\n", |
||
| 1882 | " <tr>\n", |
||
| 1883 | " <th>51</th>\n", |
||
| 1884 | " <td>R-DRE-74372</td>\n", |
||
| 1885 | " <td>Uracil + (deoxy)ribose 1-phosphate <=> (deoxy)...</td>\n", |
||
| 1886 | " <td>2</td>\n", |
||
| 1887 | " <td>2</td>\n", |
||
| 1888 | " <td>2</td>\n", |
||
| 1889 | " </tr>\n", |
||
| 1890 | " <tr>\n", |
||
| 1891 | " <th>52</th>\n", |
||
| 1892 | " <td>R-DRE-74376</td>\n", |
||
| 1893 | " <td>(deoxy)uridine + orthophosphate <=> uracil + (...</td>\n", |
||
| 1894 | " <td>2</td>\n", |
||
| 1895 | " <td>2</td>\n", |
||
| 1896 | " <td>2</td>\n", |
||
| 1897 | " </tr>\n", |
||
| 1898 | " <tr>\n", |
||
| 1899 | " <th>53</th>\n", |
||
| 1900 | " <td>R-DRE-75848</td>\n", |
||
| 1901 | " <td>Acly tetramer transforms cit to ac-coa</td>\n", |
||
| 1902 | " <td>3</td>\n", |
||
| 1903 | " <td>1</td>\n", |
||
| 1904 | " <td>1</td>\n", |
||
| 1905 | " </tr>\n", |
||
| 1906 | " <tr>\n", |
||
| 1907 | " <th>54</th>\n", |
||
| 1908 | " <td>R-DRE-75889</td>\n", |
||
| 1909 | " <td>Dhap is converted to g3p by gpd1/gpd1l</td>\n", |
||
| 1910 | " <td>2</td>\n", |
||
| 1911 | " <td>1</td>\n", |
||
| 1912 | " <td>1</td>\n", |
||
| 1913 | " </tr>\n", |
||
| 1914 | " </tbody>\n", |
||
| 1915 | "</table>\n", |
||
| 1916 | "</div>" |
||
| 1917 | ], |
||
| 1918 | "text/plain": [ |
||
| 1919 | " reaction_id reaction_name \\\n", |
||
| 1920 | "0 R-DRE-109278 Nt5e:zn2+ hydrolyses amp,damp,gmp, imp \n", |
||
| 1921 | "1 R-DRE-109291 Cmp or tmp or ump + h2o => cytidine, thymidine... \n", |
||
| 1922 | "2 R-DRE-109415 Amp + h2o => adenosine + orthophosphate [nt5c1b] \n", |
||
| 1923 | "3 R-DRE-109624 (2-deoxy)adenosine + atp => (d)amp + adp (adk) \n", |
||
| 1924 | "4 R-DRE-1237160 Mta is cleaved and phosphorylated \n", |
||
| 1925 | "5 R-DRE-1247910 Cndp2:2mn2+ dimer hydrolyses cysgly \n", |
||
| 1926 | "6 R-DRE-139970 Fmo3:fad n-oxidises tma to tmao \n", |
||
| 1927 | "7 R-DRE-1482976 Cdp-dag is converted to pi by cdipt \n", |
||
| 1928 | "8 R-DRE-1614583 Pxlp-k212-cth cleaves l-cystathionine \n", |
||
| 1929 | "9 R-DRE-174401 Ahcy:nad+ tetramer hydrolyses adohcy \n", |
||
| 1930 | "10 R-DRE-1855154 I1p is dephosphorylated to ins by impa1/2 in t... \n", |
||
| 1931 | "11 R-DRE-1855210 I3p is dephosphorylated to ins by impa1/2 in t... \n", |
||
| 1932 | "12 R-DRE-1855211 I4p is dephosphorylated to ins by impa1/2 in t... \n", |
||
| 1933 | "13 R-DRE-188467 Gly-3-p+fad->dhap+fadh2 (catalyzed by mitochon... \n", |
||
| 1934 | "14 R-DRE-197250 Nampt transfers prib to nam to form namn \n", |
||
| 1935 | "15 R-DRE-198813 Gsto dimers reduce deha to asch- \n", |
||
| 1936 | "16 R-DRE-200318 Creatine + atp => phosphocreatine + adp [ckb,ckm] \n", |
||
| 1937 | "17 R-DRE-200326 Creatine + atp => phosphocreatine + adp [ck oc... \n", |
||
| 1938 | "18 R-DRE-202127 Enos synthesizes no \n", |
||
| 1939 | "19 R-DRE-2162066 Carbovir + imp => carbovir monophosphate + ino... \n", |
||
| 1940 | "20 R-DRE-2993447 Hlcs biotinylates 6x(pcca:pccb) \n", |
||
| 1941 | "21 R-DRE-2993799 Hlcs biotinylates 6xmccc1:6xmccc2 \n", |
||
| 1942 | "22 R-DRE-3301943 Gstk1 dimer transfers gs from gsh to cdnb \n", |
||
| 1943 | "23 R-DRE-350604 Agmatine + h2o <=> putrescine + urea \n", |
||
| 1944 | "24 R-DRE-351215 Putrescine + dc-adenosyl methionine => spermi... \n", |
||
| 1945 | "25 R-DRE-372519 Accho is hydrolyzed to cho and acetate by ache \n", |
||
| 1946 | "26 R-DRE-372819 Oxaloacetate + gtp => phosphoenolpyruvate + gd... \n", |
||
| 1947 | "27 R-DRE-416530 Ffar1:ffar1 ligands activates gq \n", |
||
| 1948 | "28 R-DRE-5652172 Akr1b1 reduces glc to d-sorbitol \n", |
||
| 1949 | "29 R-DRE-5693373 Ddah1,2 hydrolyses adma to dma and l-cit \n", |
||
| 1950 | "30 R-DRE-5693724 Esd dimer hydrolyses s-fgsh to gsh \n", |
||
| 1951 | "31 R-DRE-6783221 Hagh hydrolyses (r)-s-lgsh to gsh and lact \n", |
||
| 1952 | "32 R-DRE-6783880 Pipox oxidises ppca to p6c \n", |
||
| 1953 | "33 R-DRE-6784393 Pxlp-k279-got2 dimer transaminates 4-oh-l-glut... \n", |
||
| 1954 | "34 R-DRE-6797653 Dmgdh:fad oxidatively demethylates dmgly to sarc \n", |
||
| 1955 | "35 R-DRE-6797955 Aldh7a1 oxidises betald to bet \n", |
||
| 1956 | "36 R-DRE-6798317 Gnmt tetramer transfers methyl group from adom... \n", |
||
| 1957 | "37 R-DRE-6807826 Ldhal6b reduces pyr to lact \n", |
||
| 1958 | "38 R-DRE-70342 Aldob tetramer cleaves fru-1-p to ga and dhap \n", |
||
| 1959 | "39 R-DRE-70349 Dak dimer phosphorylates d-glyceraldehyde to f... \n", |
||
| 1960 | "40 R-DRE-70510 Ldh tetramer oxidises lact to pyr \n", |
||
| 1961 | "41 R-DRE-70573 Argininosuccinate <=> fumarate + arginine \n", |
||
| 1962 | "42 R-DRE-70596 Got2 dimer deaminates l-asp \n", |
||
| 1963 | "43 R-DRE-70613 Oxaloacetate + glutamate <=> aspartate + alpha... \n", |
||
| 1964 | "44 R-DRE-70979 (s)-malate + nad+ <=> oxaloacetate + nadh + h+ \n", |
||
| 1965 | "45 R-DRE-71163 P-hydroxyphenylpyruvate + o2 => homogentisate ... \n", |
||
| 1966 | "46 R-DRE-71260 Aldh9a1 tetramer dehydrogenates teabl to form ... \n", |
||
| 1967 | "47 R-DRE-71783 Oxaloacetate + nadh + h+ <=> (s)-malate + nad+ \n", |
||
| 1968 | "48 R-DRE-71849 Ldh tetramer reduces pyr to lact \n", |
||
| 1969 | "49 R-DRE-74241 Ada catalyzes the deamination of (deoxy)adenosine \n", |
||
| 1970 | "50 R-DRE-74248 (d)gmp or (d)imp + h2o => (2-deoxy)guanosine o... \n", |
||
| 1971 | "51 R-DRE-74372 Uracil + (deoxy)ribose 1-phosphate <=> (deoxy)... \n", |
||
| 1972 | "52 R-DRE-74376 (deoxy)uridine + orthophosphate <=> uracil + (... \n", |
||
| 1973 | "53 R-DRE-75848 Acly tetramer transforms cit to ac-coa \n", |
||
| 1974 | "54 R-DRE-75889 Dhap is converted to g3p by gpd1/gpd1l \n", |
||
| 1975 | "\n", |
||
| 1976 | " num_genes num_proteins num_compounds \n", |
||
| 1977 | "0 1 1 3 \n", |
||
| 1978 | "1 1 1 2 \n", |
||
| 1979 | "2 1 1 1 \n", |
||
| 1980 | "3 1 1 1 \n", |
||
| 1981 | "4 1 1 1 \n", |
||
| 1982 | "5 1 1 1 \n", |
||
| 1983 | "6 3 1 2 \n", |
||
| 1984 | "7 1 1 1 \n", |
||
| 1985 | "8 1 1 1 \n", |
||
| 1986 | "9 1 1 1 \n", |
||
| 1987 | "10 2 1 1 \n", |
||
| 1988 | "11 2 1 1 \n", |
||
| 1989 | "12 2 1 1 \n", |
||
| 1990 | "13 1 1 1 \n", |
||
| 1991 | "14 1 1 1 \n", |
||
| 1992 | "15 2 2 1 \n", |
||
| 1993 | "16 2 2 1 \n", |
||
| 1994 | "17 1 1 1 \n", |
||
| 1995 | "18 4 2 1 \n", |
||
| 1996 | "19 1 1 1 \n", |
||
| 1997 | "20 3 1 1 \n", |
||
| 1998 | "21 3 1 1 \n", |
||
| 1999 | "22 1 1 1 \n", |
||
| 2000 | "23 1 1 1 \n", |
||
| 2001 | "24 1 1 2 \n", |
||
| 2002 | "25 2 2 2 \n", |
||
| 2003 | "26 1 1 1 \n", |
||
| 2004 | "27 5 1 1 \n", |
||
| 2005 | "28 2 1 1 \n", |
||
| 2006 | "29 1 1 1 \n", |
||
| 2007 | "30 1 1 1 \n", |
||
| 2008 | "31 1 1 1 \n", |
||
| 2009 | "32 1 1 1 \n", |
||
| 2010 | "33 2 2 1 \n", |
||
| 2011 | "34 1 1 2 \n", |
||
| 2012 | "35 1 1 1 \n", |
||
| 2013 | "36 1 1 1 \n", |
||
| 2014 | "37 1 1 1 \n", |
||
| 2015 | "38 1 1 1 \n", |
||
| 2016 | "39 1 1 1 \n", |
||
| 2017 | "40 2 2 1 \n", |
||
| 2018 | "41 1 1 1 \n", |
||
| 2019 | "42 2 2 1 \n", |
||
| 2020 | "43 2 2 1 \n", |
||
| 2021 | "44 1 1 1 \n", |
||
| 2022 | "45 1 1 1 \n", |
||
| 2023 | "46 1 1 1 \n", |
||
| 2024 | "47 1 1 1 \n", |
||
| 2025 | "48 2 2 1 \n", |
||
| 2026 | "49 1 1 2 \n", |
||
| 2027 | "50 1 1 2 \n", |
||
| 2028 | "51 2 2 2 \n", |
||
| 2029 | "52 2 2 2 \n", |
||
| 2030 | "53 3 1 1 \n", |
||
| 2031 | "54 2 1 1 " |
||
| 2032 | ] |
||
| 2033 | }, |
||
| 2034 | "execution_count": 24, |
||
| 2035 | "metadata": {}, |
||
| 2036 | "output_type": "execute_result" |
||
| 2037 | } |
||
| 2038 | ], |
||
| 2039 | "source": [ |
||
| 2040 | "reactions = m.get_nodes(types=REACTIONS)\n", |
||
| 2041 | "\n", |
||
| 2042 | "data = []\n", |
||
| 2043 | "for reaction_id, reaction_data in reactions:\n", |
||
| 2044 | " reaction_name = reaction_data['display_name']\n", |
||
| 2045 | " genes = m.get_connected(reaction_id, dest_type=GENES, observed=True)\n", |
||
| 2046 | " proteins = m.get_connected(reaction_id, dest_type=PROTEINS, observed=True)\n", |
||
| 2047 | " compounds = m.get_connected(reaction_id, dest_type=COMPOUNDS, observed=True)\n", |
||
| 2048 | " \n", |
||
| 2049 | " if len(genes) > 0 and len(proteins) > 0 and len(compounds) > 0:\n", |
||
| 2050 | " row = [reaction_id, reaction_name, len(genes), len(proteins), len(compounds)]\n", |
||
| 2051 | " data.append(row)\n", |
||
| 2052 | "\n", |
||
| 2053 | "df = pd.DataFrame(data, columns=['reaction_id', 'reaction_name', 'num_genes', 'num_proteins', 'num_compounds'])\n", |
||
| 2054 | "df" |
||
| 2055 | ] |
||
| 2056 | }, |
||
| 2057 | { |
||
| 2058 | "cell_type": "markdown", |
||
| 2059 | "metadata": {}, |
||
| 2060 | "source": [ |
||
| 2061 | "##### Find everything connected to protein 'F1QAA7'" |
||
| 2062 | ] |
||
| 2063 | }, |
||
| 2064 | { |
||
| 2065 | "cell_type": "code", |
||
| 2066 | "execution_count": 25, |
||
| 2067 | "metadata": {}, |
||
| 2068 | "outputs": [ |
||
| 2069 | { |
||
| 2070 | "data": { |
||
| 2071 | "text/html": [ |
||
| 2072 | "<div>\n", |
||
| 2073 | "<style scoped>\n", |
||
| 2074 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 2075 | " vertical-align: middle;\n", |
||
| 2076 | " }\n", |
||
| 2077 | "\n", |
||
| 2078 | " .dataframe tbody tr th {\n", |
||
| 2079 | " vertical-align: top;\n", |
||
| 2080 | " }\n", |
||
| 2081 | "\n", |
||
| 2082 | " .dataframe thead th {\n", |
||
| 2083 | " text-align: right;\n", |
||
| 2084 | " }\n", |
||
| 2085 | "</style>\n", |
||
| 2086 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 2087 | " <thead>\n", |
||
| 2088 | " <tr style=\"text-align: right;\">\n", |
||
| 2089 | " <th></th>\n", |
||
| 2090 | " <th>display_name</th>\n", |
||
| 2091 | " <th>data_type</th>\n", |
||
| 2092 | " <th>observed</th>\n", |
||
| 2093 | " <th>source_id</th>\n", |
||
| 2094 | " </tr>\n", |
||
| 2095 | " <tr>\n", |
||
| 2096 | " <th>entity_id</th>\n", |
||
| 2097 | " <th></th>\n", |
||
| 2098 | " <th></th>\n", |
||
| 2099 | " <th></th>\n", |
||
| 2100 | " <th></th>\n", |
||
| 2101 | " </tr>\n", |
||
| 2102 | " </thead>\n", |
||
| 2103 | " <tbody>\n", |
||
| 2104 | " <tr>\n", |
||
| 2105 | " <th>ENSDARG00000037781</th>\n", |
||
| 2106 | " <td>Acss2</td>\n", |
||
| 2107 | " <td>genes</td>\n", |
||
| 2108 | " <td>True</td>\n", |
||
| 2109 | " <td>F1QAA7</td>\n", |
||
| 2110 | " </tr>\n", |
||
| 2111 | " <tr>\n", |
||
| 2112 | " <th>456215</th>\n", |
||
| 2113 | " <td>Adenosine 5-monophosphate(2-)</td>\n", |
||
| 2114 | " <td>compounds</td>\n", |
||
| 2115 | " <td>False</td>\n", |
||
| 2116 | " <td>F1QAA7</td>\n", |
||
| 2117 | " </tr>\n", |
||
| 2118 | " <tr>\n", |
||
| 2119 | " <th>33019</th>\n", |
||
| 2120 | " <td>Diphosphate(3-)</td>\n", |
||
| 2121 | " <td>compounds</td>\n", |
||
| 2122 | " <td>False</td>\n", |
||
| 2123 | " <td>F1QAA7</td>\n", |
||
| 2124 | " </tr>\n", |
||
| 2125 | " <tr>\n", |
||
| 2126 | " <th>57288</th>\n", |
||
| 2127 | " <td>Acetyl-coa(4-)</td>\n", |
||
| 2128 | " <td>compounds</td>\n", |
||
| 2129 | " <td>False</td>\n", |
||
| 2130 | " <td>F1QAA7</td>\n", |
||
| 2131 | " </tr>\n", |
||
| 2132 | " <tr>\n", |
||
| 2133 | " <th>57287</th>\n", |
||
| 2134 | " <td>Coenzyme a(4-)</td>\n", |
||
| 2135 | " <td>compounds</td>\n", |
||
| 2136 | " <td>False</td>\n", |
||
| 2137 | " <td>F1QAA7</td>\n", |
||
| 2138 | " </tr>\n", |
||
| 2139 | " <tr>\n", |
||
| 2140 | " <th>30616</th>\n", |
||
| 2141 | " <td>Atp(4-)</td>\n", |
||
| 2142 | " <td>compounds</td>\n", |
||
| 2143 | " <td>False</td>\n", |
||
| 2144 | " <td>F1QAA7</td>\n", |
||
| 2145 | " </tr>\n", |
||
| 2146 | " <tr>\n", |
||
| 2147 | " <th>15366</th>\n", |
||
| 2148 | " <td>Acetic acid</td>\n", |
||
| 2149 | " <td>compounds</td>\n", |
||
| 2150 | " <td>False</td>\n", |
||
| 2151 | " <td>F1QAA7</td>\n", |
||
| 2152 | " </tr>\n", |
||
| 2153 | " <tr>\n", |
||
| 2154 | " <th>R-DRE-71735</th>\n", |
||
| 2155 | " <td>Acetate + coa + atp => acetyl-coa + amp + pyro...</td>\n", |
||
| 2156 | " <td>reactions</td>\n", |
||
| 2157 | " <td>None</td>\n", |
||
| 2158 | " <td>F1QAA7</td>\n", |
||
| 2159 | " </tr>\n", |
||
| 2160 | " <tr>\n", |
||
| 2161 | " <th>R-DRE-71384</th>\n", |
||
| 2162 | " <td>Ethanol oxidation</td>\n", |
||
| 2163 | " <td>pathways</td>\n", |
||
| 2164 | " <td>None</td>\n", |
||
| 2165 | " <td>F1QAA7</td>\n", |
||
| 2166 | " </tr>\n", |
||
| 2167 | " </tbody>\n", |
||
| 2168 | "</table>\n", |
||
| 2169 | "</div>" |
||
| 2170 | ], |
||
| 2171 | "text/plain": [ |
||
| 2172 | " display_name \\\n", |
||
| 2173 | "entity_id \n", |
||
| 2174 | "ENSDARG00000037781 Acss2 \n", |
||
| 2175 | "456215 Adenosine 5-monophosphate(2-) \n", |
||
| 2176 | "33019 Diphosphate(3-) \n", |
||
| 2177 | "57288 Acetyl-coa(4-) \n", |
||
| 2178 | "57287 Coenzyme a(4-) \n", |
||
| 2179 | "30616 Atp(4-) \n", |
||
| 2180 | "15366 Acetic acid \n", |
||
| 2181 | "R-DRE-71735 Acetate + coa + atp => acetyl-coa + amp + pyro... \n", |
||
| 2182 | "R-DRE-71384 Ethanol oxidation \n", |
||
| 2183 | "\n", |
||
| 2184 | " data_type observed source_id \n", |
||
| 2185 | "entity_id \n", |
||
| 2186 | "ENSDARG00000037781 genes True F1QAA7 \n", |
||
| 2187 | "456215 compounds False F1QAA7 \n", |
||
| 2188 | "33019 compounds False F1QAA7 \n", |
||
| 2189 | "57288 compounds False F1QAA7 \n", |
||
| 2190 | "57287 compounds False F1QAA7 \n", |
||
| 2191 | "30616 compounds False F1QAA7 \n", |
||
| 2192 | "15366 compounds False F1QAA7 \n", |
||
| 2193 | "R-DRE-71735 reactions None F1QAA7 \n", |
||
| 2194 | "R-DRE-71384 pathways None F1QAA7 " |
||
| 2195 | ] |
||
| 2196 | }, |
||
| 2197 | "execution_count": 25, |
||
| 2198 | "metadata": {}, |
||
| 2199 | "output_type": "execute_result" |
||
| 2200 | } |
||
| 2201 | ], |
||
| 2202 | "source": [ |
||
| 2203 | "query_id = 'F1QAA7'\n", |
||
| 2204 | "m.get_connected(query_id)" |
||
| 2205 | ] |
||
| 2206 | }, |
||
| 2207 | { |
||
| 2208 | "cell_type": "markdown", |
||
| 2209 | "metadata": {}, |
||
| 2210 | "source": [ |
||
| 2211 | "##### Find compounds in the data connected to protein 'F1QAA7'" |
||
| 2212 | ] |
||
| 2213 | }, |
||
| 2214 | { |
||
| 2215 | "cell_type": "code", |
||
| 2216 | "execution_count": 26, |
||
| 2217 | "metadata": {}, |
||
| 2218 | "outputs": [ |
||
| 2219 | { |
||
| 2220 | "data": { |
||
| 2221 | "text/html": [ |
||
| 2222 | "<div>\n", |
||
| 2223 | "<style scoped>\n", |
||
| 2224 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 2225 | " vertical-align: middle;\n", |
||
| 2226 | " }\n", |
||
| 2227 | "\n", |
||
| 2228 | " .dataframe tbody tr th {\n", |
||
| 2229 | " vertical-align: top;\n", |
||
| 2230 | " }\n", |
||
| 2231 | "\n", |
||
| 2232 | " .dataframe thead th {\n", |
||
| 2233 | " text-align: right;\n", |
||
| 2234 | " }\n", |
||
| 2235 | "</style>\n", |
||
| 2236 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 2237 | " <thead>\n", |
||
| 2238 | " <tr style=\"text-align: right;\">\n", |
||
| 2239 | " <th></th>\n", |
||
| 2240 | " <th>display_name</th>\n", |
||
| 2241 | " <th>data_type</th>\n", |
||
| 2242 | " <th>observed</th>\n", |
||
| 2243 | " <th>source_id</th>\n", |
||
| 2244 | " </tr>\n", |
||
| 2245 | " <tr>\n", |
||
| 2246 | " <th>entity_id</th>\n", |
||
| 2247 | " <th></th>\n", |
||
| 2248 | " <th></th>\n", |
||
| 2249 | " <th></th>\n", |
||
| 2250 | " <th></th>\n", |
||
| 2251 | " </tr>\n", |
||
| 2252 | " </thead>\n", |
||
| 2253 | " <tbody>\n", |
||
| 2254 | " <tr>\n", |
||
| 2255 | " <th>456215</th>\n", |
||
| 2256 | " <td>Adenosine 5-monophosphate(2-)</td>\n", |
||
| 2257 | " <td>compounds</td>\n", |
||
| 2258 | " <td>False</td>\n", |
||
| 2259 | " <td>F1QAA7</td>\n", |
||
| 2260 | " </tr>\n", |
||
| 2261 | " <tr>\n", |
||
| 2262 | " <th>33019</th>\n", |
||
| 2263 | " <td>Diphosphate(3-)</td>\n", |
||
| 2264 | " <td>compounds</td>\n", |
||
| 2265 | " <td>False</td>\n", |
||
| 2266 | " <td>F1QAA7</td>\n", |
||
| 2267 | " </tr>\n", |
||
| 2268 | " <tr>\n", |
||
| 2269 | " <th>57288</th>\n", |
||
| 2270 | " <td>Acetyl-coa(4-)</td>\n", |
||
| 2271 | " <td>compounds</td>\n", |
||
| 2272 | " <td>False</td>\n", |
||
| 2273 | " <td>F1QAA7</td>\n", |
||
| 2274 | " </tr>\n", |
||
| 2275 | " <tr>\n", |
||
| 2276 | " <th>57287</th>\n", |
||
| 2277 | " <td>Coenzyme a(4-)</td>\n", |
||
| 2278 | " <td>compounds</td>\n", |
||
| 2279 | " <td>False</td>\n", |
||
| 2280 | " <td>F1QAA7</td>\n", |
||
| 2281 | " </tr>\n", |
||
| 2282 | " <tr>\n", |
||
| 2283 | " <th>30616</th>\n", |
||
| 2284 | " <td>Atp(4-)</td>\n", |
||
| 2285 | " <td>compounds</td>\n", |
||
| 2286 | " <td>False</td>\n", |
||
| 2287 | " <td>F1QAA7</td>\n", |
||
| 2288 | " </tr>\n", |
||
| 2289 | " <tr>\n", |
||
| 2290 | " <th>15366</th>\n", |
||
| 2291 | " <td>Acetic acid</td>\n", |
||
| 2292 | " <td>compounds</td>\n", |
||
| 2293 | " <td>False</td>\n", |
||
| 2294 | " <td>F1QAA7</td>\n", |
||
| 2295 | " </tr>\n", |
||
| 2296 | " </tbody>\n", |
||
| 2297 | "</table>\n", |
||
| 2298 | "</div>" |
||
| 2299 | ], |
||
| 2300 | "text/plain": [ |
||
| 2301 | " display_name data_type observed source_id\n", |
||
| 2302 | "entity_id \n", |
||
| 2303 | "456215 Adenosine 5-monophosphate(2-) compounds False F1QAA7\n", |
||
| 2304 | "33019 Diphosphate(3-) compounds False F1QAA7\n", |
||
| 2305 | "57288 Acetyl-coa(4-) compounds False F1QAA7\n", |
||
| 2306 | "57287 Coenzyme a(4-) compounds False F1QAA7\n", |
||
| 2307 | "30616 Atp(4-) compounds False F1QAA7\n", |
||
| 2308 | "15366 Acetic acid compounds False F1QAA7" |
||
| 2309 | ] |
||
| 2310 | }, |
||
| 2311 | "execution_count": 26, |
||
| 2312 | "metadata": {}, |
||
| 2313 | "output_type": "execute_result" |
||
| 2314 | } |
||
| 2315 | ], |
||
| 2316 | "source": [ |
||
| 2317 | "query_id = 'F1QAA7'\n", |
||
| 2318 | "m.get_connected(query_id, dest_type=COMPOUNDS)" |
||
| 2319 | ] |
||
| 2320 | }, |
||
| 2321 | { |
||
| 2322 | "cell_type": "markdown", |
||
| 2323 | "metadata": {}, |
||
| 2324 | "source": [ |
||
| 2325 | "##### Find observed genes and proteins connected to compound '33019'" |
||
| 2326 | ] |
||
| 2327 | }, |
||
| 2328 | { |
||
| 2329 | "cell_type": "code", |
||
| 2330 | "execution_count": 27, |
||
| 2331 | "metadata": {}, |
||
| 2332 | "outputs": [ |
||
| 2333 | { |
||
| 2334 | "data": { |
||
| 2335 | "text/html": [ |
||
| 2336 | "<div>\n", |
||
| 2337 | "<style scoped>\n", |
||
| 2338 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 2339 | " vertical-align: middle;\n", |
||
| 2340 | " }\n", |
||
| 2341 | "\n", |
||
| 2342 | " .dataframe tbody tr th {\n", |
||
| 2343 | " vertical-align: top;\n", |
||
| 2344 | " }\n", |
||
| 2345 | "\n", |
||
| 2346 | " .dataframe thead th {\n", |
||
| 2347 | " text-align: right;\n", |
||
| 2348 | " }\n", |
||
| 2349 | "</style>\n", |
||
| 2350 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 2351 | " <thead>\n", |
||
| 2352 | " <tr style=\"text-align: right;\">\n", |
||
| 2353 | " <th></th>\n", |
||
| 2354 | " <th>display_name</th>\n", |
||
| 2355 | " <th>data_type</th>\n", |
||
| 2356 | " <th>observed</th>\n", |
||
| 2357 | " <th>source_id</th>\n", |
||
| 2358 | " </tr>\n", |
||
| 2359 | " <tr>\n", |
||
| 2360 | " <th>entity_id</th>\n", |
||
| 2361 | " <th></th>\n", |
||
| 2362 | " <th></th>\n", |
||
| 2363 | " <th></th>\n", |
||
| 2364 | " <th></th>\n", |
||
| 2365 | " </tr>\n", |
||
| 2366 | " </thead>\n", |
||
| 2367 | " <tbody>\n", |
||
| 2368 | " <tr>\n", |
||
| 2369 | " <th>ENSDARG00000058162</th>\n", |
||
| 2370 | " <td>Pcyt1ba</td>\n", |
||
| 2371 | " <td>genes</td>\n", |
||
| 2372 | " <td>True</td>\n", |
||
| 2373 | " <td>33019</td>\n", |
||
| 2374 | " </tr>\n", |
||
| 2375 | " <tr>\n", |
||
| 2376 | " <th>ENSDARG00000011233</th>\n", |
||
| 2377 | " <td>Pcyt1aa</td>\n", |
||
| 2378 | " <td>genes</td>\n", |
||
| 2379 | " <td>True</td>\n", |
||
| 2380 | " <td>33019</td>\n", |
||
| 2381 | " </tr>\n", |
||
| 2382 | " <tr>\n", |
||
| 2383 | " <th>ENSDARG00000004517</th>\n", |
||
| 2384 | " <td>Ppat</td>\n", |
||
| 2385 | " <td>genes</td>\n", |
||
| 2386 | " <td>True</td>\n", |
||
| 2387 | " <td>33019</td>\n", |
||
| 2388 | " </tr>\n", |
||
| 2389 | " <tr>\n", |
||
| 2390 | " <th>ENSDARG00000039934</th>\n", |
||
| 2391 | " <td>Hlcs</td>\n", |
||
| 2392 | " <td>genes</td>\n", |
||
| 2393 | " <td>True</td>\n", |
||
| 2394 | " <td>33019</td>\n", |
||
| 2395 | " </tr>\n", |
||
| 2396 | " <tr>\n", |
||
| 2397 | " <th>ENSDARG00000061994</th>\n", |
||
| 2398 | " <td>Acacb</td>\n", |
||
| 2399 | " <td>genes</td>\n", |
||
| 2400 | " <td>True</td>\n", |
||
| 2401 | " <td>33019</td>\n", |
||
| 2402 | " </tr>\n", |
||
| 2403 | " <tr>\n", |
||
| 2404 | " <th>...</th>\n", |
||
| 2405 | " <td>...</td>\n", |
||
| 2406 | " <td>...</td>\n", |
||
| 2407 | " <td>...</td>\n", |
||
| 2408 | " <td>...</td>\n", |
||
| 2409 | " </tr>\n", |
||
| 2410 | " <tr>\n", |
||
| 2411 | " <th>B0V0X1</th>\n", |
||
| 2412 | " <td>B0V0X1</td>\n", |
||
| 2413 | " <td>proteins</td>\n", |
||
| 2414 | " <td>True</td>\n", |
||
| 2415 | " <td>33019</td>\n", |
||
| 2416 | " </tr>\n", |
||
| 2417 | " <tr>\n", |
||
| 2418 | " <th>B8JLW8</th>\n", |
||
| 2419 | " <td>B8JLW8</td>\n", |
||
| 2420 | " <td>proteins</td>\n", |
||
| 2421 | " <td>True</td>\n", |
||
| 2422 | " <td>33019</td>\n", |
||
| 2423 | " </tr>\n", |
||
| 2424 | " <tr>\n", |
||
| 2425 | " <th>F1QYS7</th>\n", |
||
| 2426 | " <td>F1QYS7</td>\n", |
||
| 2427 | " <td>proteins</td>\n", |
||
| 2428 | " <td>True</td>\n", |
||
| 2429 | " <td>33019</td>\n", |
||
| 2430 | " </tr>\n", |
||
| 2431 | " <tr>\n", |
||
| 2432 | " <th>B0S5C4</th>\n", |
||
| 2433 | " <td>B0S5C4</td>\n", |
||
| 2434 | " <td>proteins</td>\n", |
||
| 2435 | " <td>True</td>\n", |
||
| 2436 | " <td>33019</td>\n", |
||
| 2437 | " </tr>\n", |
||
| 2438 | " <tr>\n", |
||
| 2439 | " <th>Q802U9</th>\n", |
||
| 2440 | " <td>Q802U9</td>\n", |
||
| 2441 | " <td>proteins</td>\n", |
||
| 2442 | " <td>True</td>\n", |
||
| 2443 | " <td>33019</td>\n", |
||
| 2444 | " </tr>\n", |
||
| 2445 | " </tbody>\n", |
||
| 2446 | "</table>\n", |
||
| 2447 | "<p>87 rows × 4 columns</p>\n", |
||
| 2448 | "</div>" |
||
| 2449 | ], |
||
| 2450 | "text/plain": [ |
||
| 2451 | " display_name data_type observed source_id\n", |
||
| 2452 | "entity_id \n", |
||
| 2453 | "ENSDARG00000058162 Pcyt1ba genes True 33019\n", |
||
| 2454 | "ENSDARG00000011233 Pcyt1aa genes True 33019\n", |
||
| 2455 | "ENSDARG00000004517 Ppat genes True 33019\n", |
||
| 2456 | "ENSDARG00000039934 Hlcs genes True 33019\n", |
||
| 2457 | "ENSDARG00000061994 Acacb genes True 33019\n", |
||
| 2458 | "... ... ... ... ...\n", |
||
| 2459 | "B0V0X1 B0V0X1 proteins True 33019\n", |
||
| 2460 | "B8JLW8 B8JLW8 proteins True 33019\n", |
||
| 2461 | "F1QYS7 F1QYS7 proteins True 33019\n", |
||
| 2462 | "B0S5C4 B0S5C4 proteins True 33019\n", |
||
| 2463 | "Q802U9 Q802U9 proteins True 33019\n", |
||
| 2464 | "\n", |
||
| 2465 | "[87 rows x 4 columns]" |
||
| 2466 | ] |
||
| 2467 | }, |
||
| 2468 | "execution_count": 27, |
||
| 2469 | "metadata": {}, |
||
| 2470 | "output_type": "execute_result" |
||
| 2471 | } |
||
| 2472 | ], |
||
| 2473 | "source": [ |
||
| 2474 | "query_id = '33019'\n", |
||
| 2475 | "genes = m.get_connected(query_id, dest_type=[GENES, PROTEINS], observed=True)\n", |
||
| 2476 | "genes" |
||
| 2477 | ] |
||
| 2478 | }, |
||
| 2479 | { |
||
| 2480 | "cell_type": "markdown", |
||
| 2481 | "metadata": {}, |
||
| 2482 | "source": [ |
||
| 2483 | "##### Find pathways connected to genes 'ENSDARG00000087927'" |
||
| 2484 | ] |
||
| 2485 | }, |
||
| 2486 | { |
||
| 2487 | "cell_type": "code", |
||
| 2488 | "execution_count": 28, |
||
| 2489 | "metadata": {}, |
||
| 2490 | "outputs": [ |
||
| 2491 | { |
||
| 2492 | "data": { |
||
| 2493 | "text/html": [ |
||
| 2494 | "<div>\n", |
||
| 2495 | "<style scoped>\n", |
||
| 2496 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 2497 | " vertical-align: middle;\n", |
||
| 2498 | " }\n", |
||
| 2499 | "\n", |
||
| 2500 | " .dataframe tbody tr th {\n", |
||
| 2501 | " vertical-align: top;\n", |
||
| 2502 | " }\n", |
||
| 2503 | "\n", |
||
| 2504 | " .dataframe thead th {\n", |
||
| 2505 | " text-align: right;\n", |
||
| 2506 | " }\n", |
||
| 2507 | "</style>\n", |
||
| 2508 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 2509 | " <thead>\n", |
||
| 2510 | " <tr style=\"text-align: right;\">\n", |
||
| 2511 | " <th></th>\n", |
||
| 2512 | " <th>display_name</th>\n", |
||
| 2513 | " <th>data_type</th>\n", |
||
| 2514 | " <th>observed</th>\n", |
||
| 2515 | " <th>source_id</th>\n", |
||
| 2516 | " </tr>\n", |
||
| 2517 | " <tr>\n", |
||
| 2518 | " <th>entity_id</th>\n", |
||
| 2519 | " <th></th>\n", |
||
| 2520 | " <th></th>\n", |
||
| 2521 | " <th></th>\n", |
||
| 2522 | " <th></th>\n", |
||
| 2523 | " </tr>\n", |
||
| 2524 | " </thead>\n", |
||
| 2525 | " <tbody>\n", |
||
| 2526 | " <tr>\n", |
||
| 2527 | " <th>R-DRE-2393930</th>\n", |
||
| 2528 | " <td>Phosphate bond hydrolysis by nudt proteins</td>\n", |
||
| 2529 | " <td>pathways</td>\n", |
||
| 2530 | " <td>None</td>\n", |
||
| 2531 | " <td>ENSDARG00000087927</td>\n", |
||
| 2532 | " </tr>\n", |
||
| 2533 | " </tbody>\n", |
||
| 2534 | "</table>\n", |
||
| 2535 | "</div>" |
||
| 2536 | ], |
||
| 2537 | "text/plain": [ |
||
| 2538 | " display_name data_type observed \\\n", |
||
| 2539 | "entity_id \n", |
||
| 2540 | "R-DRE-2393930 Phosphate bond hydrolysis by nudt proteins pathways None \n", |
||
| 2541 | "\n", |
||
| 2542 | " source_id \n", |
||
| 2543 | "entity_id \n", |
||
| 2544 | "R-DRE-2393930 ENSDARG00000087927 " |
||
| 2545 | ] |
||
| 2546 | }, |
||
| 2547 | "execution_count": 28, |
||
| 2548 | "metadata": {}, |
||
| 2549 | "output_type": "execute_result" |
||
| 2550 | } |
||
| 2551 | ], |
||
| 2552 | "source": [ |
||
| 2553 | "query_id = 'ENSDARG00000087927'\n", |
||
| 2554 | "m.get_connected(query_id, dest_type=PATHWAYS)" |
||
| 2555 | ] |
||
| 2556 | }, |
||
| 2557 | { |
||
| 2558 | "cell_type": "markdown", |
||
| 2559 | "metadata": {}, |
||
| 2560 | "source": [ |
||
| 2561 | "##### Find genes, proteins, compounds and pathways connected to reaction 'R-DRE-2395818'" |
||
| 2562 | ] |
||
| 2563 | }, |
||
| 2564 | { |
||
| 2565 | "cell_type": "code", |
||
| 2566 | "execution_count": 29, |
||
| 2567 | "metadata": {}, |
||
| 2568 | "outputs": [ |
||
| 2569 | { |
||
| 2570 | "data": { |
||
| 2571 | "text/html": [ |
||
| 2572 | "<div>\n", |
||
| 2573 | "<style scoped>\n", |
||
| 2574 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 2575 | " vertical-align: middle;\n", |
||
| 2576 | " }\n", |
||
| 2577 | "\n", |
||
| 2578 | " .dataframe tbody tr th {\n", |
||
| 2579 | " vertical-align: top;\n", |
||
| 2580 | " }\n", |
||
| 2581 | "\n", |
||
| 2582 | " .dataframe thead th {\n", |
||
| 2583 | " text-align: right;\n", |
||
| 2584 | " }\n", |
||
| 2585 | "</style>\n", |
||
| 2586 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 2587 | " <thead>\n", |
||
| 2588 | " <tr style=\"text-align: right;\">\n", |
||
| 2589 | " <th></th>\n", |
||
| 2590 | " <th>display_name</th>\n", |
||
| 2591 | " <th>data_type</th>\n", |
||
| 2592 | " <th>observed</th>\n", |
||
| 2593 | " <th>source_id</th>\n", |
||
| 2594 | " </tr>\n", |
||
| 2595 | " <tr>\n", |
||
| 2596 | " <th>entity_id</th>\n", |
||
| 2597 | " <th></th>\n", |
||
| 2598 | " <th></th>\n", |
||
| 2599 | " <th></th>\n", |
||
| 2600 | " <th></th>\n", |
||
| 2601 | " </tr>\n", |
||
| 2602 | " </thead>\n", |
||
| 2603 | " <tbody>\n", |
||
| 2604 | " <tr>\n", |
||
| 2605 | " <th>ENSDARG00000030573</th>\n", |
||
| 2606 | " <td>Nudt1</td>\n", |
||
| 2607 | " <td>genes</td>\n", |
||
| 2608 | " <td>True</td>\n", |
||
| 2609 | " <td>R-DRE-2395818</td>\n", |
||
| 2610 | " </tr>\n", |
||
| 2611 | " <tr>\n", |
||
| 2612 | " <th>Q7ZWC3</th>\n", |
||
| 2613 | " <td>Q7ZWC3</td>\n", |
||
| 2614 | " <td>proteins</td>\n", |
||
| 2615 | " <td>False</td>\n", |
||
| 2616 | " <td>R-DRE-2395818</td>\n", |
||
| 2617 | " </tr>\n", |
||
| 2618 | " <tr>\n", |
||
| 2619 | " <th>15377</th>\n", |
||
| 2620 | " <td>Water</td>\n", |
||
| 2621 | " <td>compounds</td>\n", |
||
| 2622 | " <td>False</td>\n", |
||
| 2623 | " <td>R-DRE-2395818</td>\n", |
||
| 2624 | " </tr>\n", |
||
| 2625 | " <tr>\n", |
||
| 2626 | " <th>18420</th>\n", |
||
| 2627 | " <td>Magnesium(2+)</td>\n", |
||
| 2628 | " <td>compounds</td>\n", |
||
| 2629 | " <td>False</td>\n", |
||
| 2630 | " <td>R-DRE-2395818</td>\n", |
||
| 2631 | " </tr>\n", |
||
| 2632 | " <tr>\n", |
||
| 2633 | " <th>63212</th>\n", |
||
| 2634 | " <td>2-hydroxy-damp(2-)</td>\n", |
||
| 2635 | " <td>compounds</td>\n", |
||
| 2636 | " <td>False</td>\n", |
||
| 2637 | " <td>R-DRE-2395818</td>\n", |
||
| 2638 | " </tr>\n", |
||
| 2639 | " <tr>\n", |
||
| 2640 | " <th>77897</th>\n", |
||
| 2641 | " <td>2-hydroxy-datp(4-)</td>\n", |
||
| 2642 | " <td>compounds</td>\n", |
||
| 2643 | " <td>False</td>\n", |
||
| 2644 | " <td>R-DRE-2395818</td>\n", |
||
| 2645 | " </tr>\n", |
||
| 2646 | " <tr>\n", |
||
| 2647 | " <th>15378</th>\n", |
||
| 2648 | " <td>Hydron</td>\n", |
||
| 2649 | " <td>compounds</td>\n", |
||
| 2650 | " <td>False</td>\n", |
||
| 2651 | " <td>R-DRE-2395818</td>\n", |
||
| 2652 | " </tr>\n", |
||
| 2653 | " <tr>\n", |
||
| 2654 | " <th>33019</th>\n", |
||
| 2655 | " <td>Diphosphate(3-)</td>\n", |
||
| 2656 | " <td>compounds</td>\n", |
||
| 2657 | " <td>False</td>\n", |
||
| 2658 | " <td>R-DRE-2395818</td>\n", |
||
| 2659 | " </tr>\n", |
||
| 2660 | " <tr>\n", |
||
| 2661 | " <th>R-DRE-2393930</th>\n", |
||
| 2662 | " <td>Phosphate bond hydrolysis by nudt proteins</td>\n", |
||
| 2663 | " <td>pathways</td>\n", |
||
| 2664 | " <td>None</td>\n", |
||
| 2665 | " <td>R-DRE-2395818</td>\n", |
||
| 2666 | " </tr>\n", |
||
| 2667 | " </tbody>\n", |
||
| 2668 | "</table>\n", |
||
| 2669 | "</div>" |
||
| 2670 | ], |
||
| 2671 | "text/plain": [ |
||
| 2672 | " display_name data_type \\\n", |
||
| 2673 | "entity_id \n", |
||
| 2674 | "ENSDARG00000030573 Nudt1 genes \n", |
||
| 2675 | "Q7ZWC3 Q7ZWC3 proteins \n", |
||
| 2676 | "15377 Water compounds \n", |
||
| 2677 | "18420 Magnesium(2+) compounds \n", |
||
| 2678 | "63212 2-hydroxy-damp(2-) compounds \n", |
||
| 2679 | "77897 2-hydroxy-datp(4-) compounds \n", |
||
| 2680 | "15378 Hydron compounds \n", |
||
| 2681 | "33019 Diphosphate(3-) compounds \n", |
||
| 2682 | "R-DRE-2393930 Phosphate bond hydrolysis by nudt proteins pathways \n", |
||
| 2683 | "\n", |
||
| 2684 | " observed source_id \n", |
||
| 2685 | "entity_id \n", |
||
| 2686 | "ENSDARG00000030573 True R-DRE-2395818 \n", |
||
| 2687 | "Q7ZWC3 False R-DRE-2395818 \n", |
||
| 2688 | "15377 False R-DRE-2395818 \n", |
||
| 2689 | "18420 False R-DRE-2395818 \n", |
||
| 2690 | "63212 False R-DRE-2395818 \n", |
||
| 2691 | "77897 False R-DRE-2395818 \n", |
||
| 2692 | "15378 False R-DRE-2395818 \n", |
||
| 2693 | "33019 False R-DRE-2395818 \n", |
||
| 2694 | "R-DRE-2393930 None R-DRE-2395818 " |
||
| 2695 | ] |
||
| 2696 | }, |
||
| 2697 | "execution_count": 29, |
||
| 2698 | "metadata": {}, |
||
| 2699 | "output_type": "execute_result" |
||
| 2700 | } |
||
| 2701 | ], |
||
| 2702 | "source": [ |
||
| 2703 | "m.get_connected('R-DRE-2395818')" |
||
| 2704 | ] |
||
| 2705 | }, |
||
| 2706 | { |
||
| 2707 | "cell_type": "markdown", |
||
| 2708 | "metadata": {}, |
||
| 2709 | "source": [ |
||
| 2710 | "##### Find observed genes, proteins, compounds and reactions involved in the pathway 'R-DRE-2393930'" |
||
| 2711 | ] |
||
| 2712 | }, |
||
| 2713 | { |
||
| 2714 | "cell_type": "code", |
||
| 2715 | "execution_count": 30, |
||
| 2716 | "metadata": {}, |
||
| 2717 | "outputs": [ |
||
| 2718 | { |
||
| 2719 | "data": { |
||
| 2720 | "text/html": [ |
||
| 2721 | "<div>\n", |
||
| 2722 | "<style scoped>\n", |
||
| 2723 | " .dataframe tbody tr th:only-of-type {\n", |
||
| 2724 | " vertical-align: middle;\n", |
||
| 2725 | " }\n", |
||
| 2726 | "\n", |
||
| 2727 | " .dataframe tbody tr th {\n", |
||
| 2728 | " vertical-align: top;\n", |
||
| 2729 | " }\n", |
||
| 2730 | "\n", |
||
| 2731 | " .dataframe thead th {\n", |
||
| 2732 | " text-align: right;\n", |
||
| 2733 | " }\n", |
||
| 2734 | "</style>\n", |
||
| 2735 | "<table border=\"1\" class=\"dataframe\">\n", |
||
| 2736 | " <thead>\n", |
||
| 2737 | " <tr style=\"text-align: right;\">\n", |
||
| 2738 | " <th></th>\n", |
||
| 2739 | " <th>display_name</th>\n", |
||
| 2740 | " <th>data_type</th>\n", |
||
| 2741 | " <th>observed</th>\n", |
||
| 2742 | " <th>source_id</th>\n", |
||
| 2743 | " </tr>\n", |
||
| 2744 | " <tr>\n", |
||
| 2745 | " <th>entity_id</th>\n", |
||
| 2746 | " <th></th>\n", |
||
| 2747 | " <th></th>\n", |
||
| 2748 | " <th></th>\n", |
||
| 2749 | " <th></th>\n", |
||
| 2750 | " </tr>\n", |
||
| 2751 | " </thead>\n", |
||
| 2752 | " <tbody>\n", |
||
| 2753 | " <tr>\n", |
||
| 2754 | " <th>ENSDARG00000030573</th>\n", |
||
| 2755 | " <td>Nudt1</td>\n", |
||
| 2756 | " <td>genes</td>\n", |
||
| 2757 | " <td>True</td>\n", |
||
| 2758 | " <td>R-DRE-2393930</td>\n", |
||
| 2759 | " </tr>\n", |
||
| 2760 | " <tr>\n", |
||
| 2761 | " <th>ENSDARG00000019503</th>\n", |
||
| 2762 | " <td>Zgc:103759</td>\n", |
||
| 2763 | " <td>genes</td>\n", |
||
| 2764 | " <td>True</td>\n", |
||
| 2765 | " <td>R-DRE-2393930</td>\n", |
||
| 2766 | " </tr>\n", |
||
| 2767 | " <tr>\n", |
||
| 2768 | " <th>ENSDARG00000078073</th>\n", |
||
| 2769 | " <td>Nudt5</td>\n", |
||
| 2770 | " <td>genes</td>\n", |
||
| 2771 | " <td>True</td>\n", |
||
| 2772 | " <td>R-DRE-2393930</td>\n", |
||
| 2773 | " </tr>\n", |
||
| 2774 | " <tr>\n", |
||
| 2775 | " <th>ENSDARG00000087927</th>\n", |
||
| 2776 | " <td>Nudt9</td>\n", |
||
| 2777 | " <td>genes</td>\n", |
||
| 2778 | " <td>True</td>\n", |
||
| 2779 | " <td>R-DRE-2393930</td>\n", |
||
| 2780 | " </tr>\n", |
||
| 2781 | " <tr>\n", |
||
| 2782 | " <th>ENSDARG00000041576</th>\n", |
||
| 2783 | " <td>Nudt18</td>\n", |
||
| 2784 | " <td>genes</td>\n", |
||
| 2785 | " <td>True</td>\n", |
||
| 2786 | " <td>R-DRE-2393930</td>\n", |
||
| 2787 | " </tr>\n", |
||
| 2788 | " <tr>\n", |
||
| 2789 | " <th>ENSDARG00000026090</th>\n", |
||
| 2790 | " <td>Adprm</td>\n", |
||
| 2791 | " <td>genes</td>\n", |
||
| 2792 | " <td>True</td>\n", |
||
| 2793 | " <td>R-DRE-2393930</td>\n", |
||
| 2794 | " </tr>\n", |
||
| 2795 | " <tr>\n", |
||
| 2796 | " <th>Q6IQ66</th>\n", |
||
| 2797 | " <td>Q6IQ66</td>\n", |
||
| 2798 | " <td>proteins</td>\n", |
||
| 2799 | " <td>True</td>\n", |
||
| 2800 | " <td>R-DRE-2393930</td>\n", |
||
| 2801 | " </tr>\n", |
||
| 2802 | " <tr>\n", |
||
| 2803 | " <th>F1QL34</th>\n", |
||
| 2804 | " <td>F1QL34</td>\n", |
||
| 2805 | " <td>proteins</td>\n", |
||
| 2806 | " <td>True</td>\n", |
||
| 2807 | " <td>R-DRE-2393930</td>\n", |
||
| 2808 | " </tr>\n", |
||
| 2809 | " </tbody>\n", |
||
| 2810 | "</table>\n", |
||
| 2811 | "</div>" |
||
| 2812 | ], |
||
| 2813 | "text/plain": [ |
||
| 2814 | " display_name data_type observed source_id\n", |
||
| 2815 | "entity_id \n", |
||
| 2816 | "ENSDARG00000030573 Nudt1 genes True R-DRE-2393930\n", |
||
| 2817 | "ENSDARG00000019503 Zgc:103759 genes True R-DRE-2393930\n", |
||
| 2818 | "ENSDARG00000078073 Nudt5 genes True R-DRE-2393930\n", |
||
| 2819 | "ENSDARG00000087927 Nudt9 genes True R-DRE-2393930\n", |
||
| 2820 | "ENSDARG00000041576 Nudt18 genes True R-DRE-2393930\n", |
||
| 2821 | "ENSDARG00000026090 Adprm genes True R-DRE-2393930\n", |
||
| 2822 | "Q6IQ66 Q6IQ66 proteins True R-DRE-2393930\n", |
||
| 2823 | "F1QL34 F1QL34 proteins True R-DRE-2393930" |
||
| 2824 | ] |
||
| 2825 | }, |
||
| 2826 | "execution_count": 30, |
||
| 2827 | "metadata": {}, |
||
| 2828 | "output_type": "execute_result" |
||
| 2829 | } |
||
| 2830 | ], |
||
| 2831 | "source": [ |
||
| 2832 | "m.get_connected('R-DRE-2393930', dest_type=[GENES, PROTEINS, COMPOUNDS], observed=True)" |
||
| 2833 | ] |
||
| 2834 | } |
||
| 2835 | ], |
||
| 2836 | "metadata": { |
||
| 2837 | "kernelspec": { |
||
| 2838 | "display_name": "Python 3 (ipykernel)", |
||
| 2839 | "language": "python", |
||
| 2840 | "name": "python3" |
||
| 2841 | }, |
||
| 2842 | "language_info": { |
||
| 2843 | "codemirror_mode": { |
||
| 2844 | "name": "ipython", |
||
| 2845 | "version": 3 |
||
| 2846 | }, |
||
| 2847 | "file_extension": ".py", |
||
| 2848 | "mimetype": "text/x-python", |
||
| 2849 | "name": "python", |
||
| 2850 | "nbconvert_exporter": "python", |
||
| 2851 | "pygments_lexer": "ipython3", |
||
| 2852 | "version": "3.10.1" |
||
| 2853 | } |
||
| 2854 | }, |
||
| 2855 | "nbformat": 4, |
||
| 2856 | "nbformat_minor": 4 |
||
| 2857 | } |