COEXPEDIA

Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

Sunmo Yang, Chan Yeong Kim, Sohyun Hwang, Eiru Kim, Hyojin Kim, Hongseok Shim, In suk Lee

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

The use of high-throughput array and sequencing technologies has produced unprecedented amounts of gene expression data in central public depositories, including the Gene Expression Omnibus (GEO). The immense amount of expression data in GEO provides both vast research opportunities and data analysis challenges. Co-expression analysis of highdimensional expression data has proven effective for the study of gene functions, and several coexpression databases have been developed. Here, we present a new co-expression database, COEXPEDIA (www.coexpedia.org), which is distinctive from other co-expression databases in three aspects: (i) it contains only co-functional co-expressions that passed a rigorous statistical assessment for functional association, (ii) the co-expressions were inferred from individual studies, each of which was designed to investigate gene functions with respect to a particular biomedical context such as a disease and (iii) the co-expressions are associated with medical subject headings (MeSH) that provide biomedical information for anatomical, disease, and chemical relevance. COEXPEDIA currently contains approximately eight million co-expressions inferred from 384 and 248 GEO series for humans and mice, respectively. We describe how these MeSH-associated coexpressions enable the identification of diseases and drugs previously unknown to be related to a gene or a gene group of interest.

Original languageEnglish
Pages (from-to)D389-D396
JournalNucleic Acids Research
Volume45
Issue numberD1
DOIs
Publication statusPublished - 2017 Jan 1

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Medical Subject Headings
Gene Expression
Databases
Genes
Public Opinion
Technology
Research
Pharmaceutical Preparations

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Yang, Sunmo ; Kim, Chan Yeong ; Hwang, Sohyun ; Kim, Eiru ; Kim, Hyojin ; Shim, Hongseok ; Lee, In suk. / COEXPEDIA : Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). In: Nucleic Acids Research. 2017 ; Vol. 45, No. D1. pp. D389-D396.
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COEXPEDIA : Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). / Yang, Sunmo; Kim, Chan Yeong; Hwang, Sohyun; Kim, Eiru; Kim, Hyojin; Shim, Hongseok; Lee, In suk.

In: Nucleic Acids Research, Vol. 45, No. D1, 01.01.2017, p. D389-D396.

Research output: Contribution to journalArticle

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