1 |
Batik SVG Toolkit [http://xmlgraphics.apache.org/batik].
|
2 |
Eden, E., Navon, R., Steinfeld, I., Lipson, D. and Yakhini, Z. (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10, 48.
|
3 |
Sun, H., Fang, H., Chen, T., Perkins, R. and Tong, W. (2006) GOFFA: gene ontology for functional analysis--a FDA gene ontology tool for analysis of genomic and proteomic data. BMC Bioinformatics 7(Suppl 2), S23.
DOI
|
4 |
topGO-Enrichment analysis for Gene Ontology [http://topgo.bioinf.mpi-inf.mpg.de/].
|
5 |
Graphviz-Graph Visualization Software [http://www.graphviz.org].
|
6 |
NetBeans Platform [http://platform.netbeans.org].
|
7 |
Rivals, I., Personnaz, L., Taing, L. and Potier, M. C. (2007) Enrichment or depletion of a GO category within a class of genes: which test? Bioinformatics 23, 401-407.
DOI
ScienceOn
|
8 |
The R Project for Statistical Computing [http://www.r-project. org].
|
9 |
Grossmann, S., Bauer, S., Robinson, P. N. and Vingron, M. (2007) Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics 23, 3024-3031.
DOI
ScienceOn
|
10 |
Alexa, A., Rahnenfuhrer, J. and Lengauer, T. (2006) Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22, 1600-1607.
DOI
ScienceOn
|
11 |
Noble, W. S. (2009) How does multiple testing correction work? Nature Biotechnology 27, 1135-1137.
DOI
ScienceOn
|
12 |
Eclipse RCP [http://www.eclipse.org/home/categories/rcp.php].
|
13 |
SwingsLabs Swing Component Extensions [http://java.net/ projects/swingx/].
|
14 |
NetBeans Visual Library [http://platform.netbeans.org/graph/].
|
15 |
Jackson: High-performance JSON processor [http://jackson. codehaus.org].
|
16 |
GO Slim and Subset Guide [http://www.geneontology. org/GO.slims.shtml].
|
17 |
Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Overduin, B., Pritchard, B., Riat, H. S., Rios, D., Ritchie, G. R., Ruffier, M., Schuster, M., Sobral, D., Spudich, G., Tang, Y. A., Trevanion, S., Vandrovcova, J., Vilella, A. J., White, S., Wilder, S. P., Zadissa, A., Zamora, J., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Hubbard, T. J., Parker, A., Proctor, G., Vogel, J. and Searle, S. M. (2011) Ensembl 2011. Nucleic Acids Res. 39, D800-806.
DOI
ScienceOn
|
18 |
Zeeberg, B. R., Feng, W., Wang, G., Wang, M. D., Fojo, A. T., Sunshine, M., Narasimhan, S., Kane, D. W., Reinhold, W. C., Lababidi, S., Bussey, K. J., Riss, J., Barrett, J. C. and Weinstein, J. N. (2003) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biology 4, R28.
DOI
|
19 |
Zheng, Q. and Wang, X. J. (2008) GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res. 36, W358-363.
DOI
ScienceOn
|
20 |
Beissbarth, T. and Speed, T. P. (2004) GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20, 1464-1465.
DOI
ScienceOn
|
21 |
Huang da, W., Sherman, B. T. and Lempicki, R. A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57.
DOI
ScienceOn
|
22 |
Al-Shahrour, F., Diaz-Uriarte, R. and Dopazo, J. (2004) FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20, 578-580.
DOI
ScienceOn
|
23 |
Draghici, S., Khatri, P., Bhavsar, P., Shah, A., Krawetz, S. A. and Tainsky, M. A. (2003) Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res. 31, 3775-3781.
DOI
ScienceOn
|
24 |
Bauer, S., Grossmann, S., Vingron, M. and Robinson, P. N. (2008) Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24, 1650-1651.
DOI
ScienceOn
|
25 |
Rhee, S. Y., Wood, V., Dolinski, K. and Draghici, S. (2008) Use and misuse of the gene ontology annotations. Nature reviews. Genetics 9, 509-515.
DOI
ScienceOn
|
26 |
Gene Ontology Tools [http://www.geneontology.org/GOtools. shtml].
|
27 |
Khatri, P. and Draghici, S. (2005) Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21, 3587-3595.
DOI
ScienceOn
|
28 |
Huang da, W., Sherman, B. T. and Lempicki, R. A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13.
DOI
ScienceOn
|