An equivalence approach to the integrative analysis of feature lists

BMC Bioinformatics

Table 2 Cancer Gene Lists

Set	Size	Species	Description
Atlas	989	human	Genes: hybrid gene found in at least one cancer case, or gene amplification or homozygous deletion found in a significant subset of cases in a given cancer-type.
CANgenes	189	human	191 common genes that were mutated at significant frequency in all tumors of human breast and colorectal cancers.
CIS (RTCGD)	587	multiple	Retroviral insertional mutagenesis in mouse hematopoietic tumors.
Miscellaneous	187	multiple	From Cold Spring Harbor Retroviruses Chapter on Oncogenes, an early version of the CIS database, a list from Dr. Tony Hunter, and misc. additions from the literature.
Sanger	452	human	Compilation from literature: “genes that are mutated and causally implicated in cancer development”
Vogelstein	420	human	Cancer genes related to chromosomal breakpoints
Waldman	455	Human	Gene set is from the Waldman gene database and lists cancer genes sorted by chromosomal locus and includes links to OMIM.

Cancer related genes that were used to generate a comprehensive list (allOnco) that is comprised of the union of all lists The lists have been selected from the datasets available in the file “allOnco.tsv” downloaded from the url http://www.bushmanlab.org/links/genelists. Only lists with more than 50 genes have been retained. Since the file has been downloaded the web page has changed and this file is not available anymore, although new version of the file can be found in the site

ISSN: 1471-2105