ArticleNucleic acids research2012
hiPathDB: a human-integrated pathway database with facile visualization.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Large-scale regulatory and signaling network assembly through linked open data.Database : the journal of biological databases and curation · 2021Article
- Using set theory to reduce redundancy in pathway sets.BMC bioinformatics · 2018Article
- miRTar2GO: a novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA-target interaction data.Nucleic acids research · 2017Article
- Review
- Computational dynamic approaches for temporal omics data with applications to systems medicine.BioData mining · 2017Review
- MONGKIE: an integrated tool for network analysis and visualization for multi-omics data.Biology direct · 2016Article
- Gene-based and pathway-based genome-wide association study of alcohol dependence.Shanghai archives of psychiatry · 2015Article
- PathCards: multi-source consolidation of human biological pathways.Database : the journal of biological databases and curation · 2015Article
- Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges.Database : the journal of biological databases and curation · 2015Review
- Short-term airborne particulate matter exposure alters the epigenetic landscape of human genes associated with the mitogen-activated protein kinase network: a cross-sectional study.Environmental health : a global access science source · 2014Article
- ReNE: a cytoscape plugin for regulatory network enhancement.PloS one · 2014Article
- Pathway-driven discovery of rare mutational impact on cancer.BioMed research international · 2014Article
- Integrated pathway clusters with coherent biological themes for target prioritisation.PloS one · 2014Article
- Functional characterization of motif sequences under purifying selection.Nucleic acids research · 2013Article
- Using biological pathway data with paxtools.PLoS computational biology · 2013Article
- Dynamical systems approach to endothelial heterogeneity.Circulation research · 2012Review
- Article
- Pathway Distiller - multisource biological pathway consolidation.BMC genomics · 2012Article
- IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis.BMC bioinformatics · 2012Article
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7 authors.
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Abstract
One of the biggest challenges in the study of biological regulatory networks is the systematic organization and integration of complex interactions taking place within various biological pathways. Currently, the information of the biological pathways is dispersed in multiple databases in various formats. hiPathDB is an integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. In total, it includes 1661 pathways consisting of 8976 distinct physical entities. hiPathDB provides two different types of integration. The pathway-level integration, conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account and subsequently reformatting all pathways in accordance with our model. The entity-level integration creates a single unified pathway that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Another strong merit of hiPathDB is the built-in pathway visualization module that supports explorative studies of complex networks in an interactive fashion. The layout algorithm is optimized for virtually automatic visualization of the pathways. hiPathDB is available at http://hiPathDB.kobic.re.kr.
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