Human Gene Set: IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN


Standard name IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN
Systematic name M16962
Brief description Genes down-regulated during transition from L0 (non-tumor, not infected with HCV) to L1 (non-tumor, infected with HCV) in the development of hepatocellular carcinoma.
Full description or abstract Using high-density oligonucleotide array, we comprehensively analyzed expression levels of 12600 genes in 50 hepatocellular carcinoma (HCC) samples with positive hepatitis C virus (HCV) serology (well (G1), moderately (G2), and poorly (G3) differentiated tumors) and 11 non-tumorous livers (L1 and L0) with and without HCV infection. We searched for discriminatory genes of transition (L0 vs. L1, L1 vs. G1, G1 vs. G2, G2 vs. G3) with a supervised learning method, and then arranged the samples by self-organizing map (SOM) with the discriminatory gene sets. The SOM arranged the five clusters on a unique sigmoidal curve in the order L0, L1, G1, G2, and G3. The sample arrangement reproduced development-related features of HCC such as p53 abnormality. Strikingly, G2 tumors without venous invasion were located closer to the G1 cluster, and most G2 tumors with venous invasion were located closer to the G3 cluster (P=0.001 by Fisher's exact test). Our present profiling data will serve as a framework to understand the relation between the development and dedifferentiation of HCC.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 15710396   Authors: Iizuka N,Oka M,Yamada-Okabe H,Mori N,Tamesa T,Okada T,Takemoto N,Sakamoto K,Hamada K,Ishitsuka H,Miyamoto T,Uchimura S,Hamamoto Y
Exact source Table 2: genes upregulated in L1 in comparison with L0
Related gene sets (show 7 additional gene sets from the source publication)

(show 18 gene sets from the same authors)
External links
Filtered by similarity ?
Source species Homo sapiens
Contributed by Yujin Hoshida (Broad Institute)
Source platform or
identifier namespace		 HUMAN_SEQ_ACCESSION
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 17 genes
Gene families ? Categorize these 17 genes by gene family
Show members (show 22 source identifiers mapped to 17 genes)
Version history 3.0: Renamed from LIZUKA_L0_SM_L1

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