Human Gene Set: LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q


Standard name LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q
Systematic name M8411
Brief description Genes down-regulated in urothelial cell carcinoma (UCC) tumors with LOH on 9q as compared to the tumors showing retention.
Full description or abstract We used gene expression profiling, mutation analyses of FGFR3 and TP53, and LOH analyses of chromosome 9 and the TP53 region on chromosome arm 17p, to molecularly characterize 75 Ta and T1 bladder carcinomas. We identified four major cellular processes related to cell cycle, protein synthesis, immune response, and extra cellular components that contribute to the expressional heterogeneity of early-stage urothelial cell carcinoma (UCC). Activating FGFR3 mutations were found at the highest frequency in G1 tumors (80%), and showed a strong correlation with FGFR3 expression. In contrast, G3 tumors displayed mutations in less than 10% of the cases and a low level of FGFR3 expression. Even though LOH on chromosome 9 was not associated with any specific expression pattern, our data indicate that loss of chromosome 9 is associated with tumor development rather than initiation. The combined analyses suggest the existence of two types of UCC tumors, one which is characterized by FGFR3 mutation or expression, high expression of protein synthesis genes, and low expression of cell cycle genes. Furthermore, the presented data underscore FGFR3 receptor involvement in urothelial cell transformation as the presence of FGFR3 mutations has a major impact on the global gene expression profile of bladder carcinomas.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 16532037   Authors: Lindgren D,Liedberg F,Andersson A,Chebil G,Gudjonsson S,Borg A,Månsson W,Fioretos T,Höglund M
Exact source Table 5S
Related gene sets (show 8 additional gene sets from the source publication)

(show 9 gene sets from any of these authors)
External links
Filtered by similarity ?
Source species Homo sapiens
Contributed by Arthur Liberzon (MSigDB Team)
Source platform or
identifier namespace		 Human_NCBI_Gene_ID
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 116 genes
Gene families ? Categorize these 116 genes by gene family
Show members (show 116 source identifiers mapped to 116 genes)
Version history 3.0: First introduced

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