TY - JOUR
T1 - PAGER 2.0
T2 - An update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology
AU - Yue, Zongliang
AU - Zheng, Qi
AU - Neylon, Michael T.
AU - Yoo, Minjae
AU - Shin, Jimin
AU - Zhao, Zhiying
AU - Tan, Aik Choon
AU - Chen, Jake Y.
N1 - Funding Information:
University of Alabama at Birmingham research start-up fund (to J.Y.C.) (in part); Cancer League of Colorado and the David F. and Margaret T. Grohne Family Foundation (to A.C.T.). Funding for open access charge: University of Alabama at Birmingham research start-up fund (to J.Y.C.). Conflict of interest statement. None declared.
Publisher Copyright:
© 2017 The Author(s).
PY - 2018/1/1
Y1 - 2018/1/1
N2 - Integrative Gene-set, Network and Pathway Analysis (GNPA) is a powerful data analysis approach developed to help interpret high-throughput omics data. In PAGER 1.0, we demonstrated that researchers can gain unbiased and reproducible biological insights with the introduction of PAGs (Pathways, Annotated-lists and Gene-signatures) as the basic data representation elements. In PAGER 2.0, we improve the utility of integrative GNPA by significantly expanding the coverage of PAGs and PAG-to-PAG relationships in the database, defining a new metric to quantify PAG data qualities, and developing new software features to simplify online integrative GNPA. Specifically, we included 84 282 PAGs spanning 24 different data sources that cover human diseases, published gene-expression signatures, drug-gene, miRNA-gene interactions, pathways and tissue-specific gene expressions. We introduced a new normalized Cohesion Coefficient (nCoCo) score to assess the biological relevance of genes inside a PAG, and RP-score to rank genes and assign gene-specific weights inside a PAG. The companion web interface contains numerous features to help users query and navigate the database content. The database content can be freely downloaded and is compatible with third-party Gene Set Enrichment Analysis tools. We expect PAGER 2.0 to become a major resource in integrative GNPA. PAGER 2.0 is available at http://discovery.informatics.uab.edu/PAGER/.
AB - Integrative Gene-set, Network and Pathway Analysis (GNPA) is a powerful data analysis approach developed to help interpret high-throughput omics data. In PAGER 1.0, we demonstrated that researchers can gain unbiased and reproducible biological insights with the introduction of PAGs (Pathways, Annotated-lists and Gene-signatures) as the basic data representation elements. In PAGER 2.0, we improve the utility of integrative GNPA by significantly expanding the coverage of PAGs and PAG-to-PAG relationships in the database, defining a new metric to quantify PAG data qualities, and developing new software features to simplify online integrative GNPA. Specifically, we included 84 282 PAGs spanning 24 different data sources that cover human diseases, published gene-expression signatures, drug-gene, miRNA-gene interactions, pathways and tissue-specific gene expressions. We introduced a new normalized Cohesion Coefficient (nCoCo) score to assess the biological relevance of genes inside a PAG, and RP-score to rank genes and assign gene-specific weights inside a PAG. The companion web interface contains numerous features to help users query and navigate the database content. The database content can be freely downloaded and is compatible with third-party Gene Set Enrichment Analysis tools. We expect PAGER 2.0 to become a major resource in integrative GNPA. PAGER 2.0 is available at http://discovery.informatics.uab.edu/PAGER/.
UR - http://www.scopus.com/inward/record.url?scp=85040863912&partnerID=8YFLogxK
U2 - 10.1093/nar/gkx1040
DO - 10.1093/nar/gkx1040
M3 - Article
AN - SCOPUS:85040863912
SN - 0305-1048
VL - 46
SP - D668-D676
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -
