Gene Set: LASTOWSKA_COAMPLIFIED_WITH_MYCN

Standard name LASTOWSKA_COAMPLIFIED_WITH_MYCN
Systematic name M1375
Brief description Genes co-amplified within MYCN [GeneID=4613] in primary neuroblastoma tumors.
Full description or abstract Identifying genes, whose expression is consistently altered by chromosomal gains or losses, is an important step in defining genes of biological relevance in a wide variety of tumour types. However, additional criteria are needed to discriminate further among the large number of candidate genes identified. This is particularly true for neuroblastoma, where multiple genomic copy number changes of proven prognostic value exist. We have used Affymetrix microarrays and a combination of fluorescent in situ hybridization and single nucleotide polymorphism (SNP) microarrays to establish expression profiles and delineate copy number alterations in 30 primary neuroblastomas. Correlation of microarray data with patient survival and analysis of expression within rodent neuroblastoma cell lines were then used to define further genes likely to be involved in the disease process. Using this approach, we identify >1000 genes within eight recurrent genomic alterations (loss of 1p, 3p, 4p, 10q and 11q, 2p gain, 17q gain, and the MYCN amplicon) whose expression is consistently altered by copy number change. Of these, 84 correlate with patient survival, with the minimal regions of 17q gain and 4p loss being enriched significantly for such genes. These include genes involved in RNA and DNA metabolism, and apoptosis. Orthologues of all but one of these genes on 17q are overexpressed in rodent neuroblastoma cell lines. A significant excess of SNPs whose copy number correlates with survival is also observed on proximal 4p in stage 4 tumours, and we find that deletion of 4p is associated with improved outcome in an extended cohort of tumours. These results define the major impact of genomic copy number alterations upon transcription within neuroblastoma, and highlight genes on distal 17q and proximal 4p for downstream analyses. They also suggest that integration of discriminators, such as survival and comparative gene expression, with microarray data may be useful in the identification of critical genes within regions of loss or gain in many human cancers.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 17533364   Authors: ?astowska M,Viprey V,Santibanez-Koref M,Wappler I,Peters H,Cullinane C,Roberts P,Hall AG,Tweddle DA,Pearson AD,Lewis I,Burchill SA,Jackson MS
Exact source Table 2
Related gene sets (show 2 additional gene sets from the source publication)
External links  
Filtered by similarity
Organism Homo sapiens
Contributed by Leona Saunders (MSigDB Team)
Source platform AFFY_HG_U133
Dataset references (show 1 datasets)
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 GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 43 genes
Gene families Categorize these 43 genes by gene family
Show members (show 61 members mapped to 43 genes)
Version history 3.0: First introduced

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