Citations on web-based tools

Citations on Functional profiling web-based tools

Scholar Google citations over all the references of the following tools:

Tool nameCitesReferences
GSEA  5127  
David  3531  
Babelomics  1420  
GoMiner  1043  
MappFinder  731  
GOstat  730  
OntoTools  585  
gotm  360  
WebGestalt  297  
FuncAssociate  259  
GoToolBox  227  
FunSpec  217  
GeneMerge  199  
TProfiler  116  
GProfiler  113  
GFinder  108  
Plage  97  
PathExplorer  97  
GeneTrail  95  
Goal  39  
PathExpress  36  
WebBayGoCites  29  
JProgo  26  
adgo  24  
Gazer  24  

Last update: 19-02-12 at 05:00











References:


GSEA  Cites
1.Mootha, V.K., Lindgren, C.M., Eriksson, K.F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstrale, M., Laurila, E. et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet, 34, 267-273.2009
2.Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A, 102, 15545-15550.3118

David  Cites
1.Dennis, G., Jr., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C. and Lempicki, R.A. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol, 4, P3.3144
2.Huang da, W. et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.Nucleic Acids Res 35, W169-75 (2007).139
3.Huang da, W. et al. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 8, R183 (2007).158
4.Sherman, B.T. et al. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate highthroughput gene functional analysis. BMC Bioinformatics 8, 426 (2007).90

Babelomics  Cites
1.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, 578-580.735
2.Al-Shahrour, F., Minguez, P., Tarraga, J., Medina, I., Alloza, E., Montaner, D. and Dopazo, J. (2007) FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res, 35, W91-96.138
3.Al-Shahrour, F., Minguez, P., Tarraga, J., Montaner, D., Alloza, E., Vaquerizas, J.M., Conde, L., Blaschke, C., Vera, J. and Dopazo, J. (2006) BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res, 34, W472-476.206
4.Al-Shahrour, F., Minguez, P., Vaquerizas, J.M., Conde, L. and Dopazo, J. (2005) BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res, 33, W460-464.199
5.Al‐Shahrour, F., Diaz‐Uriarte, R. and Dopazo, J. (2005) Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Bioinformatics, 21, 2988‐2993.95
6.Al‐Shahrour, F., Carbonell, J., Minguez, P., Goetz, S., Conesa, A., Tarraga, J., Medina, I.,Alloza,E., Montaner, D. and Dopazo, J. (2008) Babelomics: advanced functional profiling of transcriptomics,proteomics and genomics experiments. Nucleic Acids Res, 36, W341‐346.47

GoMiner  Cites
1.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. et al. (2003) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol, 4, R28.866
2.Zeeberg, B.R., Qin, H., Narasimhan, S., Sunshine, M., Cao, H., Kane, D.W., Reimers, M., Stephens, R.M., Bryant, D., Burt, S.K. et al. (2005) High-Throughput GoMiner, an industrial-strength integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics, 6, 168.177

MappFinder  Cites
1.Doniger, S.W., Salomonis, N., Dahlquist, K.D., Vranizan, K., Lawlor, S.C. and Conklin, B.R. (2003) MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol, 4, R7.731

GOstat  Cites
1.Beissbarth, T. and Speed, T.P. (2004) GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics, 20, 1464-1465.730

OntoTools  Cites
1.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, 3775-3781.300
2.Khatri, P., Bhavsar, P., Bawa, G. and Draghici, S. (2004) Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res, 32, W449-456.132
3.Khatri, P., Desai, V., Tarca, A.L., Sellamuthu, S., Wildman, D.E., Romero, R. and Draghici, S. (2006) New Onto‐Tools: Promoter‐Express, nsSNPCounter and Onto‐Translate. Nucleic Acids Res, 34, W626‐631.16
4.Khatri, P., Sellamuthu, S., Malhotra, P., Amin, K., Done, A. and Draghici, S. (2005) Recent additions and improvements to the Onto‐Tools. Nucleic Acids Res, 33, W762‐765.81
5.Khatri, P., Voichita, C., Kattan, K., Ansari, N., Khatri, A., Georgescu, C., Tarca, A.L. and Draghici, S. (2007) Onto‐Tools: new additions and improvements in 2006. Nucleic Acids Res, 35, W206‐211.56

gotm  Cites
1.Zhang, B., Schmoyer, D., Kirov, S. and Snoddy, J. (2004) GOTree Machine (GOTM): a web‐based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics, 5, 16.360

WebGestalt  Cites
1.Zhang, B., Kirov, S. and Snoddy, J. (2005) WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res, 33, W741‐748.297

FuncAssociate  Cites
1.Berriz, G.F., King, O.D., Bryant, B., Sander, C. and Roth, F.P. (2003) Characterizing gene sets with FuncAssociate. Bioinformatics, 19, 2502‐2504.259

GoToolBox  Cites
1.Martin, D., Brun, C., Remy, E., Mouren, P., Thieffry, D. and Jacq, B. (2004) GOToolBox: functional analysis of gene datasets based on Gene Ontology.227

FunSpec  Cites
1.Robinson, M.D., Grigull, J., Mohammad, N. and Hughes, T.R. (2002) FunSpec: a web‐based cluster interpreter for yeast. BMC Bioinformatics, 3, 35.217

GeneMerge  Cites
1.Castillo‐Davis, C.I. and Hartl, D.L. (2003) GeneMerge post‐genomic analysis, data mining, and hypothesis testing. Bioinformatics, 19, 891‐892.199

TProfiler  Cites
1.Boorsma, A., Foat, B.C., Vis, D., Klis, F. and Bussemaker, H.J. (2005) T‐profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res, 33, W592‐595.116

GProfiler  Cites
1.Reimand, J., Kull, M., Peterson, H., Hansen, J. and Vilo, J. (2007) g:Profiler‐‐a web‐based toolset for functional profiling of gene lists from large‐scale experiments. Nucleic Acids Res, 35, W193‐ 200. 113

GFinder  Cites
1.Masseroli, M., Galati, O. and Pinciroli, F. (2005) GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Res, 33, W717‐723.48
2.Masseroli, M., Martucci, D. and Pinciroli, F. (2004) GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining. Nucleic Acids Res, 32, W293‐300.60

Plage  Cites
1.Tomfohr, J., Lu, J. and Kepler, T.B. (2005) Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics, 6, 225.97

PathExplorer  Cites
1.Mlecnik, B., Scheideler, M., Hackl, H., Hartler, J., Sanchez‐Cabo, F. and Trajanoski, Z. (2005) PathwayExplorer: web service for visualizing high‐ throughput expression data on biological pathways. Nucleic Acids Res, 33, W633‐637.97

GeneTrail  Cites
1.Backes, C., Keller, A., Kuentzer, J., Kneissl, B., Comtesse, N., Elnakady, Y.A., Muller, R., Meese, E. and Lenhof, H.P. (2007) GeneTrail‐‐advanced gene set enrichment analysis. Nucleic Acids Res, 35, W186‐192.95

Goal  Cites
1.Volinia, S., Evangelisti, R., Francioso, F., Arcelli, D., Carella, M. and Gasparini, P. (2004) GOAL: automated Gene Ontology analysis of expression profiles. Nucleic Acids Res, 32, W492‐499.39

PathExpress  Cites
1.Goffard, N. and Weiller, G. (2007) PathExpress: a web‐based tool to identify relevant pathways in gene expression data. Nucleic Acids Res, 35, W176‐ 181.36

WebBayGoCites  Cites
1.Vencio, R.Z., Koide, T., Gomes, S.L. and Pereira, C.A. (2006) BayGO: Bayesian analysis of ontology term enrichment in microarray data. BMC Bioinformatics, 7, 86.29

JProgo  Cites
1.Scheer, M., Klawonn, F., Munch, R., Grote, A., Hiller, K., Choi, C., Koch, I., Schobert, M., Hartig, E., Klages, U. et al. (2006) JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res, 34, W510‐515.26

adgo  Cites
1.Nam, D., Kim, S.B., Kim, S.K., Yang, S., Kim, S.Y. and Chu, I.S. (2006) ADGO: analysis of differentially expressed gene sets using composite GO annotation. Bioinformatics, 22, 2249‐2253.24

Gazer  Cites
1.Kim, S.B., Yang, S., Kim, S.K., Kim, S.C., Woo, H.G., Volsky, D.J., Kim, S.Y. and Chu, I.S. (2007) GAzer: gene set analyzer. Bioinformatics, 23, 1697‐1699.24