Tag: Gene Function

GFICLEE 1.0 – Gene Function Inferred by Common Loss Evolutionary Events

GFICLEE 1.0

:: DESCRIPTION

GFICLEE is a program for predicting the new members in biological pathway or biological complex. It is based on the common loss events in gene evolution.

::DEVELOPER

Yang Fang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOS
  • Java

:: DOWNLOAD

GFICLEE

:: MORE INFORMATION

Citation

Fang Y, Li M, Li X, Yang Y.
GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level.
BMC Genomics. 2021 Oct 29;22(1):774. doi: 10.1186/s12864-021-08070-7. PMID: 34715785; PMCID: PMC8557005.

GenCLiP 3 – Human Gene Function And Network Analysis

GenCLiP 3

:: DESCRIPTION

GenCLiP is a literature mining tool that can cluster a list of genes with keywords that are auto-extracted from their up-to-date related literature and then manually curated by the user. GenCLiP can also generate a group of negative control genes and a group of positive control genes for comparing the cluster results with the analyzed genes to filter out un-specific keywords.

::DEVELOPER

GenCLiP team

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wang JH, Zhao LF, Wang HF, Wen YT, Jiang KK, Mao XM, Zhou ZY, Yao KT, Geng QS, Guo D, Huang ZX.
GenCLiP 3: mining human genes’ functions and regulatory networks from PubMed based on co-occurrences and natural language processing.
Bioinformatics. 2019 Nov 4:btz807. doi: 10.1093/bioinformatics/btz807. Epub ahead of print. PMID: 31681951.

Bioinformatics. 2014 Apr 23. pii: btu241. [Epub ahead of print]
GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms.
Wang JH, Zhao LF, Lin P, Su XR, Chen SJ, Huang LQ, Wang HF, Zhang H, Hu ZF, Yao KT, Huang ZX.

BMC Bioinformatics. 2008 Jul 13;9:308.
GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords.
Huang ZX, Tian HY, Hu ZF, Zhou YB, Zhao J, Yao KT.

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)

GeneMANIA 3.5.1 – Gene Function Prediction

GeneMANIA 3.5.1

:: DESCRIPTION

The GeneMANIA Cytoscape plugin brings fast gene function prediction capabilities to the desktop. GeneMANIA identifies the most related genes to a query gene set using a guilt-by-association approach. The plugin uses a large database of functional interaction networks from multiple organisms and each related gene is traceable to the source network used to make the prediction.

::DEVELOPER

Bader Lab and Morris Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GeneMANIA

:: MORE INFORMATION

Citation

GeneMANIA prediction server 2013 update.
Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W115-22. doi: 10.1093/nar/gkt533.

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.
Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD (2010)
Bioinformatics 26: 22.

GeneFAS – Gene Function Prediction

GeneFAS

:: DESCRIPTION

GeneFAS (Gene Function Annotation System) is a java based graphical user interface for prediction of gene function using multiple sources of data.

::DEVELOPER

Digital Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 GeneFAS

:: MORE INFORMATION

Citation

Joshi T, Zhang C, Lin GN, Song Z, Xu D.
GeneFAS: A tool for prediction of gene function using multiple sources of data.
Methods Mol Biol. 2008;439:369-86.