Gene Expression (Chin et al. Cancer Cell 2006)

{"longTitle":"CGH (Chin et al. Cancer Cell 2006)","cohort":"Breast Cancer (Chin 2006)","url":"http://www.ncbi.nlm.nih.gov/pubmed/17157792","probeMap":"chin2006_public/ucsfChinCGH2006Probe","dataSubType":"copy number","citation":"Cancer Cell. 2006 Dec;10(6):529-41.","label":"Copy number","articletitle":"Genomic and transcriptional aberrations linked to breast cancer pathophysiologies.","tags":["cancer"],"anatomical_origin":["Breast"],"name":"chin2006_public/ucsfChinCGH2006_genomicMatrix","dataproducer":"Chin K et. al.","sample_type":["tumor"],"type":"genomicMatrix","version":"2011-11-01","primary_disease":"breast cancer"}

{"longTitle":"CGH (Haverty et al. 2008)","cohort":"Breast Cancer (Haverty 2008)","url":"http://www.ncbi.nlm.nih.gov/pubmed/18335499","probeMap":"probeMap/probeAffy500K","dataSubType":"copy number","citation":"Genes Chromosomes Cancer. 2008 Jun;47(6):530-42","label":"Haverty CGH ","articletitle":"High-resolution genomic and expression analyses of copy number alterations in breast tumors.","tags":["cancer"],"anatomical_origin":["Breast"],"name":"haverty2008_public/haverty2008_genomicMatrix","dataproducer":"Haverty PM, Fridlyand J, Li L, Getz G, Beroukhim R, Lohr S, Wu TD, Cavet G, Zhang Z, Chant J.","wrangling_procedure":"Affymetrix 500K SNP .CEL files were downloaded from GEO (<A HREF=\"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7545\">link to GEO entry</A>). These were processed using the R package aroma.affymetrix. In brief, quantile normalization was performed, then copy number analyzed using RMA. Chip and fragment length effects were normalized out. A GLAD model was then fitted to make gain and loss calls. Finally, raw copy numbers were extracted for each probeset.","sample_type":["tumor"],"type":"genomicMatrix","wrangler":"Chris Szeto","version":"2011-11-01","primary_disease":"breast cancer"}

{"cohort":"Breast Cancer (Haverty 2008)","dataSubType":"phenotype","label":"Phenotypes","tags":["cancer"],"name":"haverty2008_public/haverty2008_public_clinicalMatrix","clinicalfeature":"haverty2008_public/haverty2008_public_clinicalFeature","type":"clinicalMatrix","wrangler":"Chris Szeto","version":"2011-11-11"}