Human Gene Set: BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_DN


Standard name BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_DN
Systematic name M4671
Brief description Down-regulated genes in non-neoplastic mucosa samples from colon cancer patients who developed recurrence of the disease.
Full description or abstract This study assessed the possibility to build a prognosis predictor, based on microarray gene expression measures, in stage II and III colon cancer patients. Tumour (T) and non-neoplastic mucosa (NM) mRNA samples from 18 patients (nine with a recurrence, nine with no recurrence) were profiled using the Affymetrix HGU133A GeneChip. The k-nearest neighbour method was used for prognosis prediction using T and NM gene expression measures. Six-fold cross-validation was applied to select the number of neighbours and the number of informative genes to include in the predictors. Based on this information, one T-based and one NM-based predictor were proposed and their accuracies were estimated by double cross-validation. In six-fold cross-validation, the lowest numbers of informative genes giving the lowest numbers of false predictions (two out of 18) were 30 and 70 with the T and NM gene expression measures, respectively. A 30-gene T-based predictor and a 70-gene NM-based predictor were then built, with estimated accuracies of 78 and 83%, respectively. This study suggests that one can build an accurate prognosis predictor for stage II and III colon cancer patients, based on gene expression measures, and one can use either tumour or non-neoplastic mucosa for this purpose.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 16091735   Authors: Barrier A,Lemoine A,Boelle PY,Tse C,Brault D,Chiappini F,Breittschneider J,Lacaine F,Houry S,Huguier M,Van der Laan MJ,Speed T,Debuire B,Flahault A,Dudoit S
Exact source Table 1: Overexpressed genes in patients who remained disease-free
Related gene sets (show 3 additional gene sets from the source publication)

(show 2 gene sets from any of these authors)
External links
Filtered by similarity ?
Source species Homo sapiens
Contributed by Leona Saunders (MSigDB Team)
Source platform or
identifier namespace		 AFFY_HG_U133
Dataset references  
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? NG-CHM interactive heatmaps
(Please note that clustering takes a few seconds)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)

Legacy heatmaps (PNG)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 30 genes
Gene families ? Categorize these 30 genes by gene family
Show members (show 35 source identifiers mapped to 30 genes)
Version history 3.0: First introduced

See MSigDB license terms here. Please note that certain gene sets have special access terms.