• PyPathway: Python Package for...

Treffer: PyPathway: Python Package for Biological Network Analysis and Visualization.

Title:
PyPathway: Python Package for Biological Network Analysis and Visualization.
Authors:
Xu Y; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology , Guangzhou Higher Education Mega Center, Guangzhou, China ., Luo XC; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology , Guangzhou Higher Education Mega Center, Guangzhou, China .
Source:
Journal of computational biology : a journal of computational molecular cell biology [J Comput Biol] 2018 May; Vol. 25 (5), pp. 499-504. Date of Electronic Publication: 2018 Apr 11.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Mary Ann Liebert, Inc Country of Publication: United States NLM ID: 9433358 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1557-8666 (Electronic) Linking ISSN: 10665277 NLM ISO Abbreviation: J Comput Biol Subsets: MEDLINE
Imprint Name(s):
Original Publication: New York, NY : Mary Ann Liebert, Inc., c1994-
MeSH Terms:
Computer Graphics* , Databases, Factual* , Gene Regulatory Networks* , Protein Interaction Maps* , Software*, Computational Biology/*methods, Computer Simulation ; Humans ; Internet
Contributed Indexing:
Keywords: enrichment analysis; network analysis; pathway; visualization
Entry Date(s):
Date Created: 20180412 Date Completed: 20190828 Latest Revision: 20190828
Update Code:
20250114
DOI:
10.1089/cmb.2017.0199
PMID:
29641230
Database:
MEDLINE

Weitere Informationen

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.