ClusterProfiler: An R package for comparing biological themes among gene clusters

OMICS A Journal of Integrative Biology

Volumn 16, Issue 5, 2012, Pages 284-287

  Yu, Guangchuang ^a   Wang, Li Gen ^b   Han, Yanyan ^a   He, Qing Yu ^a  

^a JINAN UNIVERSITY   (China)

^b Guangdong Information Center   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLUSTERPROFILER; CONTROLLED STUDY; GENE CLUSTER; GENETIC ANALYSIS; HUMAN; NONHUMAN; PRIORITY JOURNAL; WORKFLOW; YEAST;

ANIMALS; GENE EXPRESSION PROFILING; HUMANS; MICE; MULTIGENE FAMILY; PROGRAMMING LANGUAGES; PROTEOMICS; SOFTWARE; TRANSCRIPTOME; YEASTS;

MUS;

EID: 84860718683     PISSN: 15362310     EISSN: 15578100     Source Type: Journal    
DOI: 10.1089/omi.2011.0118     Document Type: Article

References (20)

1. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., et al. (2000). Gene Ontology: Tool for the unification of biology. Nat Genet 25, 25-29. (Pubitemid 30257031)
2. Asur, S., Ucar, D., and Parthasarathy, S. (2007). An ensemble framework for clustering protein-protein interaction networks. Bioinformatics 23, i29-i40. (Pubitemid 47244383)
3. Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., et al. (2009). ClueGO: A Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25, 1091-1093.
4. Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M., et al. (2004). GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20, 3710-3715. (Pubitemid 40136825)
5. Falcon, S., and Gentleman, R. (2007). Using GOstats to test gene lists for GO term association. Bioinformatics 23, 257-258. (Pubitemid 46189622)
6. Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5, R80.
7. Hosack, D.A., Dennis, G., Jr., Sherman, B.T., Lane, H.C., and Lempicki, R.A. (2003). Identifying biological themes within lists of genes with EASE. Genome Biol 4, R70.
8. Ihaka, R., and Gentleman, R. (1996). R: A language for data analysis and graphics. J Comp Graph Stat 5, 299-314.
9. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M. (2010). KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38, D355-D360.
10. Kumar, L., and Futschik, M.E. (2007). Mfuzz: A software package for soft clustering of microarray data. Bioinformation 2, 5-7.
11. Li, C., Li, X., Miao, Y., Wang, Q., Jiang, W., Xu, C., et al. (2009). SubpathwayMiner: A software package for flexible identification of pathways. Nucleic Acids Res 37, e131.
12. Osborne, J., Flatow, J., Holko, M., Lin, S., Kibbe, W., Zhu, L., et al. (2009). Annotating the human genome with Disease Ontology. BMC Genomics 10, S6.
13. Saeed, A.I., Sharov, V., White, J., Li, J, Liang, W., Bhagabati, N., et al. (2003). TM4: A free, open-source system for microarray data management and analysis. BioTechniques 34, 374-378. (Pubitemid 36184095)
14. Sánchez, A., Salicrú , M., and Ocaña, J. (2007). Statistical methods for the analysis of high-throughput data based on functional profiles derived from the Gene Ontology. J Stat Plann Inference 137, 3975-3989.
15. Schmidt, M., Böhm, D., von Tö rne, C., Steiner, E., Puhl, A., Pilch, H., et al. (2008). The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Res 68, 5405-5413.
16. Schwender, H., and Ickstadt, K. (2008). Empirical Bayes analysis of single nucleotide polymorphisms. BMC Bioinformatics 9, 144.
17. Storey, J.D. (2002). A direct approach to false discovery rates. J R Stat Soc B 64, 479-498
18. Yeung, K.Y., Medvedovic, M., and Bumgarner, R.E. (2003). Clustering gene-expression data with repeated measurements. Genome Biol 4, R34.
19. Yu, G., and He, Q.-Y. (2011). Functional similarity analysis of human virus-encoded miRNAs. J Clin Bioinformatics 1, 15.
20. Yu, G., Li, F., Qin, Y., Bo, X., Wu, Y., and Wang, S. (2010). GOSemSim: An R package formeasuring semantic similarity among GO terms and gene products. Bioinformatics 26, 976-978.