Tag: Gene Ontology

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.

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

ClueGO 2.0.5 – Cytoscape Plugin to Decipher Gene Ontology and Pathway Annotation Networks

ClueGO 2.0.5

:: DESCRIPTION

ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role.

::DEVELOPER

Integrative Cancer Immunology Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ClueGO

:: MORE INFORMATION

Citation

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J.
Bioinformatics. 2009 Apr 15;25(8):1091-3. Epub 2009 Feb 23.

SemanticSimilarity – Bien’s measure of Semantic Similarity for Gene Ontology

SemanticSimilarity

:: DESCRIPTION

SemanticSimilarity analysis facilitates automated semantic explanation of biological and clinical data annotated by biomedical ontologies. Gene Ontology (GO) becomes one of the most important biomedical ontologies with a set of controlled vocabularies, providing rich semantic annotations for genes and molecular phenotypes for diseases.

::DEVELOPER

SNUBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 SemanticSimilarity

:: MORE INFORMATION

Citation

Bien SJ, Park CH, Shim HJ, Yang W, Kim J, Kim JH.
Bi-directional semantic similarity for gene ontology to optimize biological and clinical analyses
J Am Med Inform Assoc (2012). doi:10.1136/amiajnl-2011-000659

 

CLENCH 2.0 – Calculate Cluster Enrichment using the Gene Ontology

CLENCH 2.0

:: DESCRIPTION

CLENCH is a program for calculating cluster enrichment using the Gene Ontology. Analysis of microarray data most often produces lists of genes with similar expression patterns, which are then subdivided into functional categories for biological interpretation. Such functional categorization is most commonly accomplished using Gene Ontology (GO) categories. Although there are several programs that identify and analyze functional categories for human, mouse and yeast genes none, of them accept Arabidopsis thaliana data. In order to address this need for A. thaliana community, we have developed a program that retrieves GO annotations for A. thaliana genes and performs functional category analysis for lists of genes selected by the user.

::DEVELOPER

Nigam Shah

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • perl

:: DOWNLOAD

  CLENCH

:: MORE INFORMATION

Citation

Bioinformatics. 2004 May 1;20(7):1196-7. Epub 2004 Feb 5.
CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology.
Shah NH, Fedoroff NV.

 

GOFFA – Gene Ontology for Functional Analysis

GOFFA

:: DESCRIPTION

GOFFA is a tool developed for ArrayTrack that takes a list of genes and identifies terms in Gene Ontology (GO) associated with those genes.

::DEVELOPER

the National Center for Toxicological Research (NCTR).

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 GOFFA

:: MORE INFORMATION

Citation

Sun, H., Fang, H., Chen, T., Perkings, R., and Tong, W.,
“GOFFA: Gene Ontology For Functional Analysis – Software for gene ontology-based functional analysis of genomic and proteomic data.”
BMC Bioinformatics, 7(Suppl 2):S23, 2006.

 

GO-SCAN 2.2 – Gene Ontology for Significant Collection of Annotations

GO-SCAN 2.2

:: DESCRIPTION

GO-SCAN is a bioinformatics tool that selects and presents relevant Gene Ontology (GO) annotations for a gene “hit” list from an Affymetrix microarray experiment.

GO-SCAN Online Version

::DEVELOPER

Mathematical and Statistical Computing Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • JMP

:: DOWNLOAD

 GO-SCAN

:: MORE INFORMATION

CluMa-GO 1.5 – Visualization of Mappings between the Gene Ontology and Cluster Trees

CluMa-GO 1.5

:: DESCRIPTION

CluMa-GO visualizes a large data set in the context of the Gene Ontology (GO) under consideration of a clustering of the data.

::DEVELOPER

The ISOVIS group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 CluMa-GO

:: MORE INFORMATION

Citation

CluMa-GO: Bring Gene Ontologies and Hierarchical Clusterings Together
A. Kerren, I. Jusufi, V. Aleksakhin, and F. Schreiber
Extended Abstract, BioVis 11, Providence, RI, USA, 2011.

FANN-GO – Predict Gene Ontology terms for a given protein sequence

FANN-GO

:: DESCRIPTION

FANN-GO is a Matlab software that predicts Gene Ontology terms (Molecular Function and Biological Process) for a given protein sequence.

::DEVELOPER

FANN-GO Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FANN-GO

:: MORE INFORMATION

Citation:

Proteins. 2011 Jul;79(7):2086-96. doi: 10.1002/prot.23029. Epub 2011 Apr 19.
Analysis of protein function and its prediction from amino acid sequence.
Clark WT, Radivojac P.