Tag: Gene Ontology

GOfact 20051017 – An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology

GOfact 20051017

:: DESCRIPTION

GOfact is developed to identify the functional distribution and the significantly enriched functional categories of the proteomic expression profile. It would be helpful for understanding the overall functions of these identified proteins and supply the fundamental information for further bioinformatics exploration.

::DEVELOPER

Li Dong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • Perl

:: DOWNLOAD

  GOfact

:: MORE INFORMATION

Citation

Li Dong, Li Jian-Qi, Ouyang Shu-Guang, Wang Jian, Xu Xiaojie, Zhu Yun-Ping, He Fu-Chu.
An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology.
Biochemistry and Biophysics 2005,32(11):1026-1029

HRSS 0.2 – Hybrid Relative Specificity Similarity based on Gene Ontology

HRSS 0.2

:: DESCRIPTION

HRSS provides a hybrid GO-based semantic similarity algorithm for evaluating the functional similarity between GO terms or gene products.

:: DEVELOPER

Center for Plant Environmental Sensing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL

:: DOWNLOAD

 HRSS

:: MORE INFORMATION

Citation

Wu, X., Pang, E., Lin, K. and Pei, Z.M. (2013)
Improving the Measurement of Semantic Similarity between Gene Ontology Terms and Gene Products: Insights from an Edge- and IC-Based Hybrid Method.
PLoS One 8(5), e66745. doi:10.1371/journal.pone.0066745

GO4J 1.1 – A Set of API used to Manipulate Gene Ontology Vocabulary

GO4J 1.1

:: DESCRIPTION

GO4J is a set of Java API to manipulate local GO (Gene Ontology) vocabulary. It has four features: parsing four kinds of GO defintion; organize all GO ids with directed graph; evaluating semantic similarity between any two GO ids; visualizing relations between any ids.

::DEVELOPER

 Guoqing Zhang

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 GO4J

:: MORE INFORMATION

GOBU 20200416 – Gene Ontology Browsing Utility

GOBU 20200416

:: DESCRIPTION

GOBU (Gene Ontology Browsing Utility) is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations.

::DEVELOPER

Wen-Dar Lin

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 GOBU

:: MORE INFORMATION

Citation

Lin WD, Chen YC, Ho JM, Hsiao CD.
GOBU: Toward an Integration Interface for Biological Objects.
Journal of Information Science and Engineering. 2006 22(1):19-29.

GoFish 1.11alpha – Find Genes with Combinations of Gene Ontology Attributes

GoFish 1.11alpha

:: DESCRIPTION

GoFish  selects a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes.

::DEVELOPER

Roth Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 GoFish

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Apr 12;19(6):788-9.
GoFish finds genes with combinations of Gene Ontology attributes.
Berriz GF, White JV, King OD, Roth FP.

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.

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