Tag: Pathways

MIDAS – MIning Differentially Activated Subpaths of KEGG pathways from multi-class RNA-seq data

MIDAS

:: DESCRIPTION

MIDAS is an algorithm that determines condition specific subpaths, each of which has different activities across multiple phenotypes. MIDAS utilizes gene expression quantity information fully and the network centrality information to determine condition specific subpaths.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

MIDAS

:: MORE INFORMATION

Citation

Lee S, Park Y, Kim S.
MIDAS: Mining differentially activated subpaths of KEGG pathways from multi-class RNA-seq data.
Methods. 2017 Jul 15;124:13-24. doi: 10.1016/j.ymeth.2017.05.026. Epub 2017 Jun 1. PMID: 28579402.

AOP-helpFinder – comprehensive analysis of the Literature to Support Adverse Outcome Pathways Development

AOP-helpFinder

:: DESCRIPTION

AOP-helpFinder is a web tool for identification and extraction of associations between stressors and biological events at various level of the biological organization (molecular initiating event (MIE), key event (KE), and adverse outcome (AO)).

::DEVELOPER

AOP-helpFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Jornod F, Jaylet T, Blaha L, Sarigiannis D, Tamisier L, Audouze K.
AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development.
Bioinformatics. 2021 Oct 30:btab750. doi: 10.1093/bioinformatics/btab750. Epub ahead of print. PMID: 34718414.

JEPETTO 1.3.1 – Java Enrichment of Pathways Extended To Topology

JEPETTO 1.3.1

:: DESCRIPTION

JEPETTO is a Cytoscape 3.x plugin performing integrative human gene set analysis. It identifies functional associations between genes and known cellular pathways, and processes using protein interaction networks and topological analysis.

::DEVELOPER

Interdisciplinary Computing and Complex BioSystems (ICOS) research group

:: SCREENSHOTS

JEPETTO

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 JEPETTO

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Apr 1;30(7):1029-30. doi: 10.1093/bioinformatics/btt732. Epub 2013 Dec 19.
JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks.
Winterhalter C1, Widera P, Krasnogor N.

EMPANADA – Evidence-based Assignment of Genes to Pathways in Metagenomic data

EMPANADA

:: DESCRIPTION

EMPANADA is a tool for evidence-based, non-uniform, and sample-specific assignment of gene families to pathways in metagenomic data.

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

EMPANADA

:: MORE INFORMATION

 

Blast2KEGG 0.1 – Enhanced Pathways Prediction from Nr and ENZYME Nomenclature Database

Blast2KEGG 0.1

:: DESCRIPTION

Blast2KEGG picks the enzymes from predicated genes, and performs fuzzy matching from enzyme name to EC number. It is consisted of a KEGG viewer, an annotation editor, and a genome browser. It is useful in the study of the evidence of member genes in pathways, or comparing the pathway between different species. Here is a screenshot on exploring the similarities between predicted ORFs and the reference sequences.

::DEVELOPER

qi wang

:: SCREENSHOTS

Blast2KEGG

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Java
:: DOWNLOAD

 Blast2KEGG

:: MORE INFORMATION