EMT is the dominant program in human colon cancer (Agilent)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Michael Nebozhyn
PROVIDER: E-GEOD-28722 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
EMT is the dominant program in human colon cancer.
Loboda Andre A Nebozhyn Michael V MV Watters James W JW Buser Carolyne A CA Shaw Peter Martin PM Huang Pearl S PS Van't Veer Laura L Tollenaar Rob A E M RA Jackson David B DB Agrawal Deepak D Dai Hongyue H Yeatman Timothy J TJ
BMC medical genomics 20110120
<h4>Background</h4>Colon cancer has been classically described by clinicopathologic features that permit the prediction of outcome only after surgical resection and staging.<h4>Methods</h4>We performed an unsupervised analysis of microarray data from 326 colon cancers to identify the first principal component (PC1) of the most variable set of genes. PC1 deciphered two primary, intrinsic molecular subtypes of colon cancer that predicted disease progression and recurrence.<h4>Results</h4>Here we r ...[more]
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Project description:This SuperSeries is composed of the following subset Series: GSE28567: EMT is the dominant program in human colon cancer (Affymetrix) GSE28709: EMT is the dominant program in human colon cancer (lung) GSE28722: EMT is the dominant program in human colon cancer (Agilent) Refer to individual Series
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2010-06-24 | E-GEOD-13105 | biostudies-arrayexpress
Project description:To map the genetics of gene expression in metabolically relevant tissues and investigate the diversity of expression SNPs (eSNPs) in multiple tissues from the same individual, we collected four tissues from approximately 1,000 patients undergoing Roux-en-y gastric bypass and clinical traits associated with their weight loss and co-morbidities. We then performed high-throughput genotyping and gene expression profiling and carried out a genome-wide association analyses for more than one hundred thousand gene expression traits representing four metabolically relevant tissues; liver, omental adipose, subcutaneous adipose and stomach. We successfully identified 24,531 eSNPs corresponding to ~10,000 distinct genes. This represents the greatest number of eSNPs identified to our knowledge by any study to date and the first study to identify eSNPs from stomach tissue. We then demonstrate how these eSNPs provide a high quality disease map for each tissue in morbidly obese patients to not only inform genetic associations indentified in this cohort, but in previously published genome wide association studies as well. eSNPs and gene co-expression modules identification in morbidly obese patients represent a great resource that will aid in elucidating the key networks associated with morbid obesity, response to RYGB and disease as a whole. Keywords: Tissue profiling in a human cohort. Liver tissue was collected from patients at the time of RYGB surgery at Massachusetts General Hospital between 2000 and 2007. Samples were collected in RNAlater (Ambion/Applied Biosystems), stored at -80° and shipped to Rosetta Inpharmatics Gene Expression Laboratory Seattle, WA for extraction, amplification, labeling, and microarray processing. Samples processed ranged in size from 100-200mg. Total RNA extracted from liver was converted to fluorescently labeled cRNA that was hybridized to custom 44K DNA oligonucleotide microarrays manufactured by Agilent Technologies as described previously (Hughes et al. 2001; Schadt et al. 2008). Successful gene expression profiling results were collected from 651 liver samples.
2011-04-01 | E-GEOD-24293 | biostudies-arrayexpress
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2011-04-01 | E-GEOD-24297 | biostudies-arrayexpress
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