PathwaysWeb 2.0 – Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning

PathwaysWeb 2.0

:: DESCRIPTION

PathwaysWeb provides publicly available information on genes, biological pathways, Gene Ontology terms, gene gene interaction networks with interaction directionality, and links to related PubMed documents.

::DEVELOPER

PathwaysWeb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PathwaysWeb: A Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning.
Melott JM, Weinstein JN, Broom BM.
Bioinformatics. 2015 Sep 23. pii: btv554.

GOseq 1.44.0 – Performing Gene Ontology (GO) based tests on RNA-seq data

GOseq 1.44.0

:: DESCRIPTION

GOseq is an R library for performing Gene Ontology (GO) and other category based tests on RNA-seq data, which corrects for selection bias.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GOseq

:: MORE INFORMATION

Citation

Gene ontology analysis for RNA-seq: accounting for selection bias
Matthew D. Young, Matthew J. Wakefield, Gordon K. Smyth, Alicia Oshlack
Genome Biology 2010, 11:R14 (4 February 2010)

Ontologizer 2.1 – Analysis and Visualization of High-Throughput Biological Data Using Gene Ontology

Ontologizer 2.1

:: DESCRIPTION

Ontologizer is a Java webstart application for GO term enrichment analysis that provides browsing and graph visualization capabilities. The Ontologizer allows users to analyze data with the standard Fisher exact test and also the parent-child method and topology methods.

::DEVELOPER

The Computational Biology @ Charité Berlin

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

  Ontologizer

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 15;24(14):1650-1. Epub 2008 May 29.
Ontologizer 2.0–a multifunctional tool for GO term enrichment analysis and data exploration.
Bauer S, Grossmann S, Vingron M, Robinson PN.

GOTreePlus 20080131 – Interactive Gene Ontology Browser

GOTreePlus 20080131

:: DESCRIPTION

GOTreePlus is an interactive gene ontology visualization tool that can superimpose annotation information over gene ontology structures. GOTreePlus can facilitate the identification of important GO terms while visualizing them in the gene ontology structure. The interactive pie chart summary for a selected gene ontology term provides users with a succinct overview of their experimental results.

::DEVELOPER

SNU HCI LAB

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET Framework 2.0

:: DOWNLOAD

 GOTreePlus

:: MORE INFORMATION

Citation

Bongshin Lee, Kristy Brown, Yetrib Hathout, and Jinwook Seo,
GOTreePlus: An Interactive Gene Ontology Browser,”
Bioinformatics (2008) 24 (7): 1026-1028.

A-DaGO-Fun / DaGO-Fun – Gene Ontology Semantic Similarity based Functional Analysis

A-DaGO-Fun / DaGO-Fun

:: DESCRIPTION

A-DaGO-Fun is a python library that provides a comprehensive and customized set of Gene Ontology (GO) based functional analysis tools that exploit the biological knowledge that GO offers in describing genes or groups of genes through the use of GO semantic similarity measures for biological knowledge discovery.

The DaGO-Fun tool is a an integrated set of GO-based functional analysis tools incorporating the large amounts of biological knowledge that GO offers in describing genes or groups of genes.

::DEVELOPER

The UCT Computational Biology Group (CBIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

A-DaGO-Fun: An adaptable Gene Ontology semantic similarity based functional analysis tool.
Mazandu GK, Chimusa ER, Mbiyavanga M, Mulder NJ.
Bioinformatics. 2015 Oct 17. pii: btv590.

DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.
Mazandu GK, Mulder NJ.
BMC Bioinformatics. 2013 Sep 25;14:284. doi: 10.1186/1471-2105-14-284.

GOGO – Measure Semantic Similarity between Gene Ontology terms

GOGO

:: DESCRIPTION

GOGO is an improved algorithm to measure the semantic similarity of gene ontology terms

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

GOGO

:: MORE INFORMATION

Citation

Zhao C, Wang Z.
GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms.
Sci Rep. 2018 Oct 10;8(1):15107. doi: 10.1038/s41598-018-33219-y. PMID: 30305653; PMCID: PMC6180005.

CateGOrizer 3.218 – Gene Ontology (GO) Terms Classifications Tool

CateGOrizer 3.218

:: DESCRIPTION

CateGOrizer, previously known as “GO Terms Classifications Counter”, is a free web tool for users to batch analyze GO term data sets in terms of GO classes they represent.

::DEVELOPER

NAGRP Bioinformatics Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Zhi-Liang Hu, Jie Bao and James M. Reecy (2008)
CateGOrizer: A Web-Based Program to Batch Analyze Gene Ontology Classification Categories“.
Online J Bioinform. 9 (2):108-112.

Csbl.go 1.4.1 – Gene Ontology based Clustering using semantic Similarity

Csbl.go 1.4.1

:: DESCRIPTION

Csbl.go is an R package for computing semantic similarity between genes using Gene Ontology annotation and for clustering genes based on the similarity measures. The package also includes GO enrichment analysis functionality.

::DEVELOPER

Hautaniemi Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R Package

:: DOWNLOAD

 Csbl.go

:: MORE INFORMATION

Citation

Fast Gene Ontology based clustering for microarray experiments
Kristian Ovaska, Marko Laakso and Sampsa Hautaniemi
BioData Mining 2008, 1:11

Argot2 – Functional Annotation of Proteins using the Semantic Similarity in the Gene Ontology

Argot2

:: DESCRIPTION

Argot2 (Annotation Retrieval of Genel Ontology Terms) is able to quickly process thousands of sequences for functional inference. The tool exploits a combined approach based on the clustering process of GO terms dependent on their semantic similarities and a weighting scheme which assesses retrieved hits sharing a certain degree of biological features with the sequence to annotate.

::DEVELOPER

Argot2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S14. doi: 10.1186/1471-2105-13-S4-S14.
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.
Falda M1, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, Cilia E, Velasco R, Fontana P.

GOssTo 1.01 – the Gene Ontology Semantic Similarity Tool

GOssTo 1.01

:: DESCRIPTION

GOssTo is a Java based semantic similarity calculator. Bundled in the software are the well-known Resnik, Lin, Jian, simUI, simGRASM similarity measures. It features powerful extension capabilities allowing the user to add as many similarity measures as needed.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

  GOssTo

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 22. [Epub ahead of print]
GOssTo: a user-friendly stand-alone and web tool for calculating semantic similarities on the Gene Ontology.
Caniza H1, Romero AE, Heron S, Yang H, Devoto A, Frasca M, Mesiti M, Valentini G, Paccanaro A.