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Open AccessJournal ArticleDOI

NetPath: a public resource of curated signal transduction pathways

Kumaran Kandasamy, +40 more
- 12 Jan 2010 - 
- Vol. 11, Iss: 1, pp 1-9
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TLDR
NetPath provides detailed maps of a number of immune signaling pathways, which include approximately 1,600 reactions annotated from the literature and more than 2,800 instances of transcriptionally regulated genes - all linked to over 5,500 published articles.
Abstract: 
We have developed NetPath as a resource of curated human signaling pathways. As an initial step, NetPath provides detailed maps of a number of immune signaling pathways, which include approximately 1,600 reactions annotated from the literature and more than 2,800 instances of transcriptionally regulated genes - all linked to over 5,500 published articles. We anticipate NetPath to become a consolidated resource for human signaling pathways that should enable systems biology approaches.

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Association analysis identifies 65 new breast cancer risk loci

Kyriaki Michailidou, +396 more
- 02 Nov 2017 - 
TL;DR: A genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry finds that heritability of Breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2–5-fold enriched relative to the genome- wide average.
Journal ArticleDOI

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

Jüri Reimand, +12 more
- 01 Feb 2019 - 
TL;DR: This protocol describes pathway enrichment analysis of gene lists from RNA-seq and other genomics experiments using g:Profiler, GSEA, Cytoscape and EnrichmentMap software, and describes innovative visualization techniques.
Journal ArticleDOI

Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review

Peter Csermely, +6 more
- 01 Jun 2013 - 
TL;DR: It is shown how network techniques can help in the identification of single-target, edgetic, multi-target and allo-network drug target candidates and an optimized protocol of network-aided drug development is suggested, and a list of systems-level hallmarks of drug quality is provided.
Journal ArticleDOI

The BioPAX community standard for pathway data sharing

Emek Demir, +94 more
- 01 Sep 2010 - 
TL;DR: Thousands of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases, and this large amount of pathway data in a computable form will support visualization, analysis and biological discovery.
Journal ArticleDOI

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

Steven Xijin Ge, +2 more
- 19 Dec 2018 - 
TL;DR: iDEP helps unveil the multifaceted functions of p53 and the possible involvement of several microRNAs such as miR-92a, miR/Bioconductor packages, 2 web services, and comprehensive annotation and pathway databases for 220 plant and animal species.
References
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Journal ArticleDOI

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

Paul Shannon, +8 more
- 01 Nov 2003 - 
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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Minoru Kanehisa, +1 more
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TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Michael Hucka, +43 more
- 01 Mar 2003 - 
TL;DR: This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
Journal ArticleDOI

Human Protein Reference Database—2009 update

T. S. Keshava Prasad, +31 more
- 01 Jan 2009 - 
TL;DR: A number of new features in HPRD are added, including PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest, and a protein distributed annotation system—Human Proteinpedia.
Journal ArticleDOI

PANTHER: a library of protein families and subfamilies indexed by function.

Paul Thomas, +8 more
- 01 Sep 2003 - 
TL;DR: The PANTHER/X ontology is used to give a high-level representation of gene function across the human and mouse genomes, and the family HMMs are used to rank missense single nucleotide polymorphisms (SNPs) according to their likelihood of affecting protein function.
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