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Nucleic Acids Res. 2018 Jan 4;46(D1):D668-D676. doi: 10.1093/nar/gkx1040.

PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology.

Author information

1
Informatics Institute, School of Medicine, the University of Alabama at Birmingham, AL 35294, USA.
2
School of Information Science and Technology, Guangdong University of Foreign Studies, Guangzhou, Guangdong 510006, China.
3
Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.
4
Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
5
School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China.

Abstract

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/.

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