Challenges of the information age: the impact of false discovery on pathway identification

BMC Research Notes

Mary E Edgerton¹  Srinivasa C Chekuri¹  Colin J Rog¹ 

[1] M.D. Anderson Cancer Center, Department of Pathology, 1515 Holcombe Blvd, Houston, TX, 77030, USA

关键词: Cancer pathways;    Bioinformatics;    Networks;    Genes;    Pathways;    Databases;   

Others  :  1165170
DOI  :  10.1186/1756-0500-5-647

 received in 2012-09-11, accepted in 2012-11-16,  发布年份 2012

【 摘 要 】

Background

Pathways with members that have known relevance to a disease are used to support hypotheses generated from analyses of gene expression and proteomic studies. Using cancer as an example, the pitfalls of searching pathways databases as support for genes and proteins that could represent false discoveries are explored.

Findings

The frequency with which networks could be generated from 100 instances each of randomly selected five and ten genes sets as input to MetaCore, a commercial pathways database, was measured. A PubMed search enumerated cancer-related literature published for any gene in the networks. Using three, two, and one maximum intervening step between input genes to populate the network, networks were generated with frequencies of 97%, 77%, and 7% using ten gene sets and 73%, 27%, and 1% using five gene sets. PubMed reported an average of 4225 cancer-related articles per network gene.

Discussion

This can be attributed to the richly populated pathways databases and the interest in the molecular basis of cancer. As information sources become enriched, they are more likely to generate plausible mechanisms for false discoveries.

【 授权许可】

   
2012 Rog et al.; licensee BioMed Central Ltd.

【 图 表 】

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