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Gene expression data from 62 colorectal cancers

ABSTRACT: We stratified colorectal tumor samples using a new unsupervised, iterative method based on non-negative matrix factorization (NMF). The resulting five subtypes exhibited activation of specific signaling pathways, and significant differences in microsatellite status and tumor location. We could also align three CRC cell lines panels to these subtypes. mRNA from 62 colorectal tumor samples was hybridized to Affymetrix HGU133 Plus 2.0 expression arrays. Log2 gene expression values were calculated using RMA.

ORGANISM(S): Homo sapiens

SUBMITTER: Garry Beran

PROVIDER: E-GEOD-35896 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines.

Schlicker Andreas A Beran Garry G Chresta Christine M CM McWalter Gael G Pritchard Alison A Weston Susie S Runswick Sarah S Davenport Sara S Heathcote Kerry K Castro Denis Alferez DA Orphanides George G French Tim T Wessels Lodewyk F A LF

BMC medical genomics 20121231

<h4>Background</h4>Colorectal cancer (CRC) is a heterogeneous and biologically poorly understood disease. To tailor CRC treatment, it is essential to first model this heterogeneity by defining subtypes of patients with homogeneous biological and clinical characteristics and second match these subtypes to cell lines for which extensive pharmacological data is available, thus linking targeted therapies to patients most likely to respond to treatment.<h4>Methods</h4>We applied a new unsupervised, i ...[more]

PMID: 23272949

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