GOrilla – Gene Ontology enRIchment anaLysis and visuaLizAtion tool

GOrilla

:: DESCRIPTION

GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (e.g. by level of expression or of differential expression).

::DEVELOPER

Yakhini Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson and Zohar Yakhini.
GOrilla: A Tool For Discovery And Visualization of Enriched GO Terms in Ranked Gene Lists“,
BMC Bioinformatics 2009, 10:48.

GOMEP – Gene Ontology-based Missing Enzyme Predictor

GOMEP

:: DESCRIPTION

GOMEP Predicts Missing Enzymes using functional coherence scores of Gene Ontology (GO) terms

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

GOMEP

:: MORE INFORMATION

Citation

Sci Rep. 2016 Aug 24;6:31725. doi: 10.1038/srep31725.
Missing gene identification using functional coherence scores.
Chitale M, Khan IK, Kihara D

NaviGO – An analytic tool for Gene Ontology Visualization and Similarity

NaviGO

:: DESCRIPTION

NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.
Wei Q, Khan IK, Ding Z, Yerneni S, Kihara D.
BMC Bioinformatics. 2017 Mar 20;18(1):177. doi: 10.1186/s12859-017-1600-5.

PhyloPFP – Gene Ontology Prediction Using Phylogenomics

PhyloPFP

:: DESCRIPTION

PhyloPFP is a phylogenomics based protein function prediction server

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Mar 1;35(5):753-759. doi: 10.1093/bioinformatics/bty704.
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences.
Jain A, Kihara D.

GoSurfer 2.0 – Graphical Data Mining tool for Microarray data using Gene Ontology Information

GoSurfer 2.0

:: DESCRIPTION

GoSurfer uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GoSurfer

:: MORE INFORMATION

Citation

Zhong S, Storch F, Lipan O, Kao MJ, Weitz C, Wong WH.
GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space.
Applied Bioinformatics 2004, 3(4): 1-5.

GOtcha 200812 – Prediction of Gene Function by Application of Gene Ontology

GOtcha 200812

:: DESCRIPTION

GOtcha uses sequence similarity searches to associate GO terms with your sequence. These are ranked by probability and displayed graphically on a subtree of Gene Ontology.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GOtcha

:: MORE INFORMATION

Citation

Martin,DMA, Berriman, M and Barton, GJ (2004),
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes,
BMC Bioinformatics, 5:178 (18 November 2004)

gowinda 1.12 – Gene Ontology Term Enrichment for Genome Wide Association Studies

gowinda 1.12

:: DESCRIPTION

Gowinda is a multi-threaded Java application that allows an unbiased analysis of gene set enrichment for Genome Wide Association Studies.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • Python

:: DOWNLOAD

 gowinda

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Aug 1;28(15):2084-5. doi: 10.1093/bioinformatics/bts315. Epub 2012 May 26.
Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.
Kofler R1, Schlötterer C.

MANGO – Prediction of Protein Function from Manually Annotated proteins based on GO (Gene Ontology)

MANGO

:: DESCRIPTION

MANGO is a server for predicting functional class of a protein. It predict function according to GO categories. The method is developed on protein in UNIPROT database whoes function have been assigned manually according to GO criteria.

::DEVELOPER

Dr. G P S Raghava,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2006)
MANGO: prediction of Genome Ontology (GO) class of a protein from its amino acid and dipeptide composition using nearest neighbor approach.
CASP7: 93

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

The State Key Laboratory of Proteomics, Beijing Proteome Research Center (BPRC)

:: 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

GOExtender 20151030 – Extending Gene Ontology with Gene Association Networks

GOExtender 20151030

:: DESCRIPTION

GOExtender is a new algorithm to efficiently identify all the connected gene pairs labeled by the same parent Gene Ontology (GO) terms.

::DEVELOPER

Jiajie Peng (jiajiepeng@hit.edu.cn), Chen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • JRE

:: DOWNLOAD

 GOExtender

:: MORE INFORMATION

Citation

Extending Gene Ontology with Gene Association Networks.
Peng J, Wang T, Wang J, Wang Y, Chen J.
Bioinformatics. 2015 Dec 7. pii: btv712.