Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

paper Cited Public

Authors: Syed, Adnan S; D'Antonio, Matteo; Ciccarelli, Francesca D
Year: 2010
Journal: Nucleic acids research
PMID: 19906700
DOI: 10.1093/nar/gkp957
PMCID: PMC2808873

#	Section	Preview
0	INTRODUCTION	Cancer is a genetic disease caused by the accumulation of deleterious modifications within the…
1	INTRODUCTION	mutated in breast, colorectal, pancreatic cancers and glioblastoma (6–8). Furthermore, the pilot…
2	INTRODUCTION	A number of databases have been set up over the years to collect and organize several types of…
3	INTRODUCTION	Protein interactions have been successfully used to infer functional links between proteins (25). In…
4	MATERIALS AND METHODS — Dataset of human cancer genes	We define cancer genes as a collection of 736 genes that are mutated in different cancer types and…
5	MATERIALS AND METHODS — Gene duplicability	We define gene duplicability as in Rambaldi et al. (11). In brief, we first align the protein…
6	MATERIALS AND METHODS — Orthology assignment and evolutionary appearance	We derive the orthology relationships from the eggNOG database (32). Based on these relationships,…
7	MATERIALS AND METHODS — Orthology assignment and evolutionary appearance	Depending on the number of paralogs of a given cancer gene at each branch, we also derive the…
8	MATERIALS AND METHODS — Protein interaction network	In order to gather the most complete representation of the human protein–protein interaction…
9	MATERIALS AND METHODS — Protein interaction network	January 2009706622 1191374MINT (36)5 February 2009515112 6531210DIP (37)26 January…
10	MATERIALS AND METHODS — Protein interaction network	Given the poor overlap between the five data sets (Table 1), their integration allows a more…
11	MATERIALS AND METHODS — Database description	NCG is divided into four sections: (i) the gene summary table, which allows the conversion between…
12	RESULTS AND DISCUSSION — Information retrieval	NCG allows retrieving information on cancer genes in three ways: (i) by using different types of…
13	RESULTS AND DISCUSSION — Duplicability of cancer genes	In accordance with our previous report (11), at 60% coverage we find 104 duplicable cancer genes…
14	RESULTS AND DISCUSSION — Duplicability of cancer genes	In the case of the tumor suppressor gene PTEN, we find an almost identical duplicate (97% coverage,…
15	RESULTS AND DISCUSSION — Orthologs and evolutionary appearance of cancer genes	NCG collects orthology information for 723 out of 736 cancer genes (98.2%), since 13 genes are not…
16	RESULTS AND DISCUSSION — Orthologs and evolutionary appearance of cancer genes	As expected for an enzyme-coding gene, orthologs of PTEN are detectable in all branches of the tree…
17	RESULTS AND DISCUSSION — Network properties of cancer proteins	For each of the 579 cancer proteins with available network information (78.7% of the total), we…
18	RESULTS AND DISCUSSION — Network properties of cancer proteins	Overall, we find 619 human hubs, 78 of which are cancer proteins (13.4% of the total set). This…
19	RESULTS AND DISCUSSION — Network properties of cancer proteins	The PTEN has overall 35 interactors, 21 of which are hubs. This, together with a high betweenness…

Name	Type
ADAM29 local	gene
ANKFN1 local	gene
Arabidopsis thaliana	cohort
breast cancer	phenotype
cancer	phenotype
Cancer Gene Census local	cohort
cancer genes local	cohort
cancer genes local	gene
Cancer Genome Project local	cohort
cancer proteins local	phenotype
Candidate Cancer Genes local	gene
CAN-genes local	cohort
CGC-genes local	cohort
colorectal cancer	phenotype
Danio rerio	cohort
disease genes	gene
duplicable cancer genes local	gene
Ensembl	drug
Entrez local	drug
glioblastoma	phenotype
HPRD local	drug
human hubs local	cohort
human protein–protein interaction network local	cohort
lung adenocarcinoma	phenotype
NCG local	cohort
NCG local	drug
Network of Cancer Genes (NCG) local	cohort
OMIM local	drug
pancreatic cancer	phenotype
PDGFRB local	gene
protein	drug
PTEN	gene
PTENP1	gene
RefSeq local	drug
RefSeq database local	drug
STK11	gene
TP53	gene
TSP-genes local	cohort
TSP-genes local	gene
Tumor Sequencing Project local	cohort
Tumor Sequencing Project genes local	gene
Tyrosine phosphatases local	drug

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