Dataset Information

Extracting consistent knowledge from highly inconsistent cancer gene data sources.

ABSTRACT:

Background

Hundreds of genes that are causally implicated in oncogenesis have been found and collected in various databases. For efficient application of these abundant but diverse data sources, it is of fundamental importance to evaluate their consistency.

Results

First, we showed that the lists of cancer genes from some major data sources were highly inconsistent in terms of overlapping genes. In particular, most cancer genes accumulated in previous small-scale studies could not be rediscovered in current high-throughput genome screening studies. Then, based on a metric proposed in this study, we showed that most cancer gene lists from different data sources were highly functionally consistent. Finally, we extracted functionally consistent cancer genes from various data sources and collected them in our database F-Census.

Conclusions

Although they have very low gene overlapping, most cancer gene data sources are highly consistent at the functional level, which indicates that they can separately capture partial genes in a few key pathways associated with cancer. Our results suggest that the sample sizes currently used for cancer studies might be inadequate for consistently capturing individual cancer genes, but could be sufficient for finding a number of cancer genes that could represent functionally most cancer genes. The F-Census database provides biologists with a useful tool for browsing and extracting functionally consistent cancer genes from various data sources.

SUBMITTER: Gong X

PROVIDER: S-EPMC2832783 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature

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Publications

Extracting consistent knowledge from highly inconsistent cancer gene data sources.

Gong Xue X Wu Ruihong R Zhang Yuannv Y Zhao Wenyuan W Cheng Lixin L Gu Yunyan Y Zhang Lin L Wang Jing J Zhu Jing J Guo Zheng Z

BMC bioinformatics 20100205

<h4>Background</h4>Hundreds of genes that are causally implicated in oncogenesis have been found and collected in various databases. For efficient application of these abundant but diverse data sources, it is of fundamental importance to evaluate their consistency.<h4>Results</h4>First, we showed that the lists of cancer genes from some major data sources were highly inconsistent in terms of overlapping genes. In particular, most cancer genes accumulated in previous small-scale studies could not ...[more]

PMID: 20137077

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Dataset Information

Extracting consistent knowledge from highly inconsistent cancer gene data sources.

Background

Results

Conclusions

Publications

Extracting consistent knowledge from highly inconsistent cancer gene data sources.

Similar Datasets

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