Help:Tools using WikiPathways

From WikiPathways

List of bioinformatics software tools using WikiPathways

PathVisio

PathVisio is a tool for displaying and editing biological pathways. In a sense PathVisio lets you draw pathways as you would in any drawing program, like PowerPoint or Photoshop. But the difference is that PathVisio can understand the biological context of a pathway, because you can link biological entities (genes or proteins) in your pathways to biological data using database identifiers. This will let you map experimental data (e.g. microarray data) and visualize it on top of the pathway drawing.

Cytoscape

Cytoscape is an open source software platform for visualizing complex-networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web. WikiPathways can be easily imported via web services using the WikiPathways app. Pathways in gpml format created in PathVisio or WikiPathways can be loaded as either their native diagram format or as simplified network graphs, supporting either data visualization or network analysis and augmentation use cases. A brief tutorial is available on OpenTutorials and a detailed description of the app and its usage was published in the Cytoscape App Collection in F1000Research.

GO-Elite

GO-Elite is a software tool designed to identify a minimal non-redundant set of Gene Ontology (GO) biological terms or pathways to describe a particular set of genes. GO-Elite uses WikiPathways as its official pathway source. GO-Elite is also available as a Cytoscape plugin.

AltAnalyze

AltAnalyze is an easy-to-use application for the end-to-end analysis of microarry, single-cell (ICGS) and bulk RNA-Seq data. AltAnalyze uses WikiPathways as its official pathway source.

SNPLogic

The purpose of SNPLogic is to provide comprehensive interactive SNP annotation, selection and prioritization system for focused genotyping projects and/or analysis and interpretation of SNP data. The user can create one or more SNP lists and populate them by adding SNPs either directly or by picking genes, pathways, chromosomal locations or by uploading own SNP lists.

WebGestalt

WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". It is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources, including WikiPathways, and provides an easy way for biologists to make sense out of gene lists.

Agilent Technologies

Agilent Technologies produces commercial sequencing technology and analysis suites (GeneSpring and EnViz) that uses WikiPathways content via web services.

Enrichr

Enrichr is a comprehensive gene set enrichment analysis web server. Includes WikiPathways as one of their data sources.

BioServices

BioServices is a Python package that provides access to many Bioinformatics Web Services (including WikiPathways) and a framework to easily implement Web Service wrappers (based on WSDL/SOAP or REST protocols).

EuGene

Eu.Gene Analyzer is an easy-to-use, stand-alone application that allows rapid and powerful microarray data analysis in the context of biological pathways. Its intuitive graphical user interface makes it an easy and flexible tool, even for the first-time user. Pathways can be downloaded from WikiPathways in EuGene's .pwf format.

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List of databases and resources that include WikiPathways content

PCxN

Generates a co-activity map across pathways, assessing the correlation based on gene content within and across pathway resources.

Pathprint

Pathprinting integrates pathway curation, profiling methods, and public repositories, to represent any expression profile as a ternary score (-1, 0, +1) in a standardized pathway panel.

BioPortal

Use BioPortal to access and share ontologies that are actively used in biomedical communities. WikiPathways uses BioPortal to power its ontology tagging system and BioPortal lists all ontology-tagged pathways as resources.

ConsensusPathDB

ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions, as well as interactions that we have curated from literature, including WikiPathways.

Wikipedia

The free encyclopedia that anyone can edit. In collaboration with MCB and GeneWiki, we have added interactive pathway maps using WikiPathways (example).

NCBI Biosystems

The NCBI BioSystems Database is a centralized repository containing biological pathways from several resources and connects those with associated literature, molecular and chemical data throughout the Entrez system. This makes it possible to link to WikiPathways directly from NCBI pages. Whether you are browsing Gene, Pubchem or Structure entities at NCBI, you will find relevant summaries, images and links to WikiPathways. They are listed as "Pathways from BioSystems" under the "General gene information" section (example). You can also view information about a single pathway on the summary pages and browse our pathway content by gene, pubchem or structure frequency.

Gene Wiki

Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.

IMPaLA

IMPaLA is a web tool, developed for integrated pathway analysis of metabolomics data alongside gene expression or protein abundance data. It works through extending over-representation and enrichment analyses to multiple data types. It uses pathway data from several different online pathway databases, including WikiPathways.

NIF

The NIF (Neuroscience Information Framework) is a dynamic inventory of web-based neuroscience resources. WikiPathways is included as one of the resources.

Pathway Commons

Pathway Commons aims to store and disseminate knowledge about biological pathways, and includes pathway data from multiple sources, including WikiPathways.

Therapeutic Targets Database

TTD is a database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets.

SkeletonGenetics

Database for genes and mutations related to genetic skeletal disorders. Displays WikiPathways data via WebGestalt.

Lynx: an Integrated Systems Biology Platform

Lynx is a database and knowledge extraction engine for integrative medicine.

miRNA Pathway Dictionary Database (miRPathDB)

miRPathDB aims to augment available target pathway web-servers by providing researches easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific the regulations are.

IRNdb

IRNdb is a database that combines microRNA, PIWI-interacting RNAs, and long non-coding RNA information with immunologically relevant target genes. The database is intended to advance research on the influence of ncRNAs on immunological processes, and includes WikiPathways as a data source.

MetaboLights

MetaboLights is a database for Metabolomics experiments and derived information. It lists more then 20 thousand metabolites and for each in which pathways they are found, deriving from pathways from WikiPathways and Reactome.