BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

被引：3235

作者：

Maere, S ^{[1
]}

Heymans, K ^{[1
]}

Kuiper, M ^{[1
]}

机构：

[1] State Univ Ghent VIB, Dept Plant Syst Biol, B-9052 Ghent, Belgium

来源：

BIOINFORMATICS | 2005年 / 21卷 / 16期

关键词：

D O I：

10.1093/bioinformatics/bti551

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape's versatile visualization environment to produce an intuitive and customizable visual representation of the results.

引用

收藏

页码：3448 / 3449

页数：2

相关论文

共 13 条

[1] FatiGO:: a web tool for finding significant associations of Gene Ontology terms with groups of genes [J].

Al-Shahrour, F ;

Díaz-Uriarte, R ;

Dopazo, J .

BIOINFORMATICS, 2004, 20 (04) :578-580

[2] An automated method for finding molecular complexes in large protein interaction networks [J].

Bader, GD ;

Hogue, CW .

BMC BIOINFORMATICS, 2003, 4 (1)

[3] GOstat: find statistically overrepresented Gene Ontologies within a group of genes [J].

Beissbarth, T ;

Speed, TP .

BIOINFORMATICS, 2004, 20 (09) :1464-1465

[4]

Benjamini Y, 2001, ANN STAT, V29, P1165

[5] Characterizing gene sets with FuncAssociate [J].

Berriz, GF ;

King, OD ;

Bryant, B ;

Sander, C ;

Roth, FP .

BIOINFORMATICS, 2003, 19 (18) :2502-2504

[6] GO::TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes [J].

Boyle, EI ;

Weng, SA ;

Gollub, J ;

Jin, H ;

Botstein, D ;

Cherry, JM ;

Sherlock, G .

BIOINFORMATICS, 2004, 20 (18) :3710-3715

[7]

Ge Y, 2003, 633 UC BERK DEP STAT

[8] Identifying biological themes within lists of genes with EASE [J].

Hosack, DA ;

Dennis, G ;

Sherman, BT ;

Lane, HC ;

Lempicki, RA .

GENOME BIOLOGY, 2003, 4 (10)

[9] GFINDer:: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining [J].

Masseroli, M ;

Martucci, D ;

Pinciroli, F .

NUCLEIC ACIDS RESEARCH, 2004, 32 :W293-W300

[10] The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes [J].

Ruepp, A ;

Zollner, A ;

Maier, D ;

Albermann, K ;

Hani, J ;

Mokrejs, M ;

Tetko, I ;

Güldener, U ;

Mannhaupt, G ;

Münsterkötter, M ;

Mewes, HW .

NUCLEIC ACIDS RESEARCH, 2004, 32 (18) :5539-5545