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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W416-21. doi: 10.1093/nar/gku368. Epub 2014 May 9.

OncoSearch: cancer gene search engine with literature evidence.

Author information

1
Department of Computer Science, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
2
School of Information and Communications, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 500-712, Republic of Korea.
3
Department of Computer Science, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea park@cs.kaist.ac.kr.

Abstract

In order to identify genes that are involved in oncogenesis and to understand how such genes affect cancers, abnormal gene expressions in cancers are actively studied. For an efficient access to the results of such studies that are reported in biomedical literature, the relevant information is accumulated via text-mining tools and made available through the Web. However, current Web tools are not yet tailored enough to allow queries that specify how a cancer changes along with the change in gene expression level, which is an important piece of information to understand an involved gene's role in cancer progression or regression. OncoSearch is a Web-based engine that searches Medline abstracts for sentences that mention gene expression changes in cancers, with queries that specify (i) whether a gene expression level is up-regulated or down-regulated, (ii) whether a certain type of cancer progresses or regresses along with such gene expression change and (iii) the expected role of the gene in the cancer. OncoSearch is available through http://oncosearch.biopathway.org.

PMID:
24813447
PMCID:
PMC4086113
DOI:
10.1093/nar/gku368
[Indexed for MEDLINE]
Free PMC Article

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