Text Mining in Cancer Gene and Pathway Prioritization

Overview

Journal Cancer Inform

Publisher Sage Publications

Specialty Biomedical Engineering

Date 2014 Nov 14

PMID 25392685

Citations 17

Authors

Yuan Luo

Gregory Riedlinger

Peter Szolovits

Affiliations

Soon will be listed here.

Abstract

Prioritization of cancer implicated genes has received growing attention as an effective way to reduce wet lab cost by computational analysis that ranks candidate genes according to the likelihood that experimental verifications will succeed. A multitude of gene prioritization tools have been developed, each integrating different data sources covering gene sequences, differential expressions, function annotations, gene regulations, protein domains, protein interactions, and pathways. This review places existing gene prioritization tools against the backdrop of an integrative Omic hierarchy view toward cancer and focuses on the analysis of their text mining components. We explain the relatively slow progress of text mining in gene prioritization, identify several challenges to current text mining methods, and highlight a few directions where more effective text mining algorithms may improve the overall prioritization task and where prioritizing the pathways may be more desirable than prioritizing only genes.

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