Standard name |
NIKOLSKY_BREAST_CANCER_21Q22_AMPLICON |
Systematic name |
M5718 |
Brief description |
Genes within amplicon 21q22 identified in a copy alterations study of 191 breast tumor samples. |
Full description or abstract |
A single cancer cell contains large numbers of genetic alterations that in combination create the malignant phenotype. However, whether amplified and mutated genes form functional and physical interaction networks that could explain the selection for cells with combined alterations is unknown. To investigate this issue, we characterized copy number alterations in 191 breast tumors using dense single nucleotide polymorphism arrays and identified 1,747 genes with copy number gain organized into 30 amplicons. Amplicons were distributed unequally throughout the genome. Each amplicon had distinct enrichment pattern in pathways, networks, and molecular functions, but genes within individual amplicons did not form coherent functional units. Genes in amplicons included all major tumorigenic pathways and were highly enriched in breast cancer-causative genes. In contrast, 1,188 genes with somatic mutations in breast cancer were distributed randomly over the genome, did not represent a functionally cohesive gene set, and were relatively less enriched in breast cancer marker genes. Mutated and gained genes did not show statistically significant overlap but were highly synergistic in populating key tumorigenic pathways including transforming growth factor beta, WNT, fibroblast growth factor, and PIP3 signaling. In general, mutated genes were more frequently upstream of gained genes in transcription regulation signaling than vice versa, suggesting that mutated genes are mainly regulators, whereas gained genes are mostly regulated. ESR1 was the major transcription factor regulating amplified but not mutated genes. Our results support the hypothesis that multiple genetic events, including copy number gains and somatic mutations, are necessary for establishing the malignant cell phenotype. |
Collection |
C2: Curated CGP: Chemical and Genetic Perturbations |
Source publication |
Pubmed 19010930 Authors: Nikolsky Y,Sviridov E,Yao J,Dosymbekov D,Ustyansky V,Kaznacheev V,Dezso Z,Mulvey L,Macconaill LE,Winckler W,Serebryiskaya T,Nikolskaya T,Polyak K |
Exact source |
Suppl. Excel File 1S: 21q22 |
Related gene sets |
(show 30 additional gene sets from the source publication)
(show 12 gene sets from the same authors)
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External links |
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Source species |
Homo sapiens |
Contributed by |
Jessica Robertson (MSigDB Team) |
Source platform or identifier namespace |
Human_NCBI_Gene_ID |
Dataset references |
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Compendia expression profiles ? |
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
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these 16 genes
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Gene families ? |
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16 genes by gene family
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Show members |
(show 16 source identifiers mapped to 16 genes)
Source Id |
NCBI (Entrez) Gene Id |
Gene Symbol |
Gene Description |
104 |
104 |
ADARB1 |
adenosine deaminase RNA specific B1 [So... |
10841 |
10841 |
FTCD |
formimidoyltransferase cyclodeaminase [... |
1291 |
1291 |
COL6A1 |
collagen type VI alpha 1 chain [Source:... |
1292 |
1292 |
COL6A2 |
collagen type VI alpha 2 chain [Source:... |
23181 |
23181 |
DIP2A |
disco interacting protein 2 homolog A [... |
23275 |
23275 |
POFUT2 |
protein O-fucosyltransferase 2 [Source:... |
378832 |
378832 |
COL18A1-AS1 |
COL18A1 antisense RNA 1 [Source:HGNC Sy... |
4047 |
4047 |
LSS |
lanosterol synthase [Source:HGNC Symbol... |
5116 |
5116 |
PCNT |
pericentrin [Source:HGNC Symbol;Acc:HGN... |
54039 |
54039 |
PCBP3 |
poly(rC) binding protein 3 [Source:HGNC... |
54058 |
54058 |
C21orf58 |
chromosome 21 open reading frame 58 [So... |
54059 |
54059 |
YBEY |
ybeY metalloendoribonuclease [Source:HG... |
6573 |
6573 |
SLC19A1 |
solute carrier family 19 member 1 [Sour... |
80781 |
80781 |
COL18A1 |
collagen type XVIII alpha 1 chain [Sour... |
84221 |
84221 |
SPATC1L |
spermatogenesis and centriole associate... |
8888 |
8888 |
MCM3AP |
minichromosome maintenance complex comp... |
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Version history |
3.0: First introduced
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