MiRGator v2.0: An integrated system for functional investigation of microRNAs

Sooyoung Cho; Yukyung Jun; Sanghyun Lee; Hyung Seok Choi; Sungchul Jung; Youngjun Jang; Charny Park; Sangok Kim; Sanghyuk Lee; Wankyu Kim

doi:10.1093/nar/gkq1094

MiRGator v2.0: An integrated system for functional investigation of microRNAs

Sooyoung Cho, Yukyung Jun, Sanghyun Lee, Hyung Seok Choi, Sungchul Jung, Youngjun Jang, Charny Park, Sangok Kim, Sanghyuk Lee, Wankyu Kim

Department of Life Science

Research output: Contribution to journal › Article › peer-review

52 Scopus citations

Abstract

MiRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation, which aims to facilitate functional investigation of miRNAs. The recent version of miRGator v2.0 contains information about (i) human miRNA expression profiles under various experimental conditions, (ii) paired expression profiles of both mRNAs and miRNAs, (iii) gene expression profiles under miRNA-perturbation (e.g. miRNA knockout and overexpression), (iv) known/predicted miRNA targets and (v) miRNA-disease associations. In total, >8000 miRNA expression profiles, ̃300 miRNA-perturbed gene expression profiles and ̃2000 mRNA expression profiles are compiled with manually curated annotations on disease, tissue type and perturbation. By integrating these data sets, a series of novel associations (miRNA-miRNA, miRNA-disease and miRNA-target) is extracted via shared features. For example, differentially expressed genes (DEGs) after miRNA knockout were systematically compared against miRNA targets. Likewise, differentially expressed miRNAs (DEmiRs) were compared with disease-associated miRNAs. Additionally, miRNA expression and disease-phenotype profiles revealed miRNA pairs whose expression was regulated in parallel in various experimental and disease conditions. Complex associations are readily accessible using an interactive network visualization interface. The miRGator v2.0 serves as a reference database to investigate miRNA expression and function (http://miRGator.kobic.re.kr).

Original language	English
Pages (from-to)	D158-D162
Journal	Nucleic Acids Research
Volume	39
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkq1094
State	Published - Jan 2011

Bibliographical note

Funding Information:
GIST Systems Biology Infrastructure Establishment Grant (2010) through Ewha Research Center for Systems Biology (ERCSB); Biogreen 21 Program of the Korean Rural Development Administration (20070401034010); National Core Research Center (NCRC) program (R15-2006-020) of the KOSEF funded by the MEST. Funding for open access charge: GIST Systems Biology Infrastructure Establishment Grant (2010) through Ewha Research Center for Systems Biology (ERCSB).

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title = "MiRGator v2.0: An integrated system for functional investigation of microRNAs",

abstract = "MiRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation, which aims to facilitate functional investigation of miRNAs. The recent version of miRGator v2.0 contains information about (i) human miRNA expression profiles under various experimental conditions, (ii) paired expression profiles of both mRNAs and miRNAs, (iii) gene expression profiles under miRNA-perturbation (e.g. miRNA knockout and overexpression), (iv) known/predicted miRNA targets and (v) miRNA-disease associations. In total, >8000 miRNA expression profiles,{\~ }300 miRNA-perturbed gene expression profiles and{\~ }2000 mRNA expression profiles are compiled with manually curated annotations on disease, tissue type and perturbation. By integrating these data sets, a series of novel associations (miRNA-miRNA, miRNA-disease and miRNA-target) is extracted via shared features. For example, differentially expressed genes (DEGs) after miRNA knockout were systematically compared against miRNA targets. Likewise, differentially expressed miRNAs (DEmiRs) were compared with disease-associated miRNAs. Additionally, miRNA expression and disease-phenotype profiles revealed miRNA pairs whose expression was regulated in parallel in various experimental and disease conditions. Complex associations are readily accessible using an interactive network visualization interface. The miRGator v2.0 serves as a reference database to investigate miRNA expression and function (http://miRGator.kobic.re.kr).",

author = "Sooyoung Cho and Yukyung Jun and Sanghyun Lee and Choi, {Hyung Seok} and Sungchul Jung and Youngjun Jang and Charny Park and Sangok Kim and Sanghyuk Lee and Wankyu Kim",

note = "Funding Information: GIST Systems Biology Infrastructure Establishment Grant (2010) through Ewha Research Center for Systems Biology (ERCSB); Biogreen 21 Program of the Korean Rural Development Administration (20070401034010); National Core Research Center (NCRC) program (R15-2006-020) of the KOSEF funded by the MEST. Funding for open access charge: GIST Systems Biology Infrastructure Establishment Grant (2010) through Ewha Research Center for Systems Biology (ERCSB).",

year = "2011",

month = jan,

doi = "10.1093/nar/gkq1094",

language = "English",

volume = "39",

pages = "D158--D162",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "SUPPL. 1",

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T2 - An integrated system for functional investigation of microRNAs

AU - Cho, Sooyoung

AU - Jun, Yukyung

AU - Lee, Sanghyun

AU - Choi, Hyung Seok

AU - Jung, Sungchul

AU - Jang, Youngjun

AU - Park, Charny

AU - Kim, Sangok

AU - Lee, Sanghyuk

AU - Kim, Wankyu

N1 - Funding Information: GIST Systems Biology Infrastructure Establishment Grant (2010) through Ewha Research Center for Systems Biology (ERCSB); Biogreen 21 Program of the Korean Rural Development Administration (20070401034010); National Core Research Center (NCRC) program (R15-2006-020) of the KOSEF funded by the MEST. Funding for open access charge: GIST Systems Biology Infrastructure Establishment Grant (2010) through Ewha Research Center for Systems Biology (ERCSB).

PY - 2011/1

Y1 - 2011/1

N2 - MiRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation, which aims to facilitate functional investigation of miRNAs. The recent version of miRGator v2.0 contains information about (i) human miRNA expression profiles under various experimental conditions, (ii) paired expression profiles of both mRNAs and miRNAs, (iii) gene expression profiles under miRNA-perturbation (e.g. miRNA knockout and overexpression), (iv) known/predicted miRNA targets and (v) miRNA-disease associations. In total, >8000 miRNA expression profiles, ̃300 miRNA-perturbed gene expression profiles and ̃2000 mRNA expression profiles are compiled with manually curated annotations on disease, tissue type and perturbation. By integrating these data sets, a series of novel associations (miRNA-miRNA, miRNA-disease and miRNA-target) is extracted via shared features. For example, differentially expressed genes (DEGs) after miRNA knockout were systematically compared against miRNA targets. Likewise, differentially expressed miRNAs (DEmiRs) were compared with disease-associated miRNAs. Additionally, miRNA expression and disease-phenotype profiles revealed miRNA pairs whose expression was regulated in parallel in various experimental and disease conditions. Complex associations are readily accessible using an interactive network visualization interface. The miRGator v2.0 serves as a reference database to investigate miRNA expression and function (http://miRGator.kobic.re.kr).

AB - MiRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation, which aims to facilitate functional investigation of miRNAs. The recent version of miRGator v2.0 contains information about (i) human miRNA expression profiles under various experimental conditions, (ii) paired expression profiles of both mRNAs and miRNAs, (iii) gene expression profiles under miRNA-perturbation (e.g. miRNA knockout and overexpression), (iv) known/predicted miRNA targets and (v) miRNA-disease associations. In total, >8000 miRNA expression profiles, ̃300 miRNA-perturbed gene expression profiles and ̃2000 mRNA expression profiles are compiled with manually curated annotations on disease, tissue type and perturbation. By integrating these data sets, a series of novel associations (miRNA-miRNA, miRNA-disease and miRNA-target) is extracted via shared features. For example, differentially expressed genes (DEGs) after miRNA knockout were systematically compared against miRNA targets. Likewise, differentially expressed miRNAs (DEmiRs) were compared with disease-associated miRNAs. Additionally, miRNA expression and disease-phenotype profiles revealed miRNA pairs whose expression was regulated in parallel in various experimental and disease conditions. Complex associations are readily accessible using an interactive network visualization interface. The miRGator v2.0 serves as a reference database to investigate miRNA expression and function (http://miRGator.kobic.re.kr).

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U2 - 10.1093/nar/gkq1094

DO - 10.1093/nar/gkq1094

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SP - D158-D162

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - SUPPL. 1

ER -

MiRGator v2.0: An integrated system for functional investigation of microRNAs

Abstract

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