CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Shoemaker, Jason E ^a   Lopes, Tiago J S ^a   Ghosh, Samik ^b   Matsuoka, Yukiko ^a,b   Kawaoka, Yoshihiro ^a,c,d   Kitano, Hiroaki ^a,b,e,f  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b Systems Biology Institute   (Japan)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

^d UNIVERSITY OF TOKYO   (Japan)

^e SONY COMPUTER SCIENCE LABORATORIES INC   (Japan)

^f OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

Author keywords

Cell type enrichment; Deconvolution; Influenza; Microarray data; Systems immunology

Indexed keywords

ANIMAL CELL; ARTICLE; BIOINFORMATICS; CELL TYPE; COMPUTER PROGRAM; CTEN SOFTWARE; GENE CLUSTER; GENE EXPRESSION; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; INNATE IMMUNITY; LYMPHOCYTE; LYMPHOCYTE COUNT; MICROARRAY ANALYSIS; MOUSE; NONHUMAN;

COMPUTATIONAL BIOLOGY; HUMANS; INTERNET; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 84865743056     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-460     Document Type: Article

References (26)

1. Hacia JG, Fan JB, Ryder O, Jin L, Edgemon K, Ghandour G, Mayer RA, Sun B, Hsie L, Robbins CM, et al. Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat Genet 1999, 22(2):164-167. 10.1038/9674, 10369258.
2. Shao L, Fan X, Cheng N, Wu L, Xiong H, Fang H, Ding D, Shi L, Cheng Y, Tong W. Shifting from population-wide to personalized cancer prognosis with microarrays. PLoS One 2012, 7(1):e29534. 10.1371/journal.pone.0029534, 3266237, 22295060.
3. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004, 101(16):6062-6067. 10.1073/pnas.0400782101, 395923, 15075390.
4. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102(43):15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
5. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29.
6. Chang JT, Nevins JR. GATHER: a systems approach to interpreting genomic signatures. Bioinformatics 2006, 22(23):2926-2933. 10.1093/bioinformatics/btl483, 17000751.
7. da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57.
8. Kaimal V, Bardes EE, Tabar SC, Jegga AG, Aronow BJ. ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems. Nucleic Acids Res 2010, 38:W96-102. 10.1093/nar/gkq418, 2896202, 20484371.
9. Baas T, Baskin CR, Diamond DL, Garcia-Sastre A, Bielefeldt-Ohmann H, Tumpey TM, Thomas MJ, Carter VS, Teal TH, Van Hoeven N, et al. Integrated molecular signature of disease: analysis of influenza virus-infected macaques through functional genomics and proteomics. J Virol 2006, 80(21):10813-10828. 10.1128/JVI.00851-06, 1641753, 16928763.
10. Schwartz R, Shackney SE. Applying unmixing to gene expression data for tumor phylogeny inference. BMC Bioinforma 2010, 11:42.
11. Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM, Butte AJ. Cell type-specific gene expression differences in complex tissues. Nat Methods 2010, 7(4):287-289. 10.1038/nmeth.1439, 20208531.
12. McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA. The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res 2011, 39:D1011-1015. Database issue, 10.1093/nar/gkq1259, 3013751, 21177656.
13. Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, et al. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 2009, 10(11):R130. 10.1186/gb-2009-10-11-r130, 3091323, 19919682.
14. Eisenberg E, Levanon EY. Human housekeeping genes are compact. Trends Genet 2003, 19(7):362-365. 10.1016/S0168-9525(03)00140-9, 12850439.
15. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinforma 2008, 9:559.
16. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
17. Team RDC R: A Language and Environment for Statistical Computing 2010, R Foundation for Statistical Computing, Vienna, Austria, Team RDC.
18. da Huang W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009, 37(1):1-13. 10.1093/nar/gkn923, 2615629, 19033363.
19. Medzhitov R. Recognition of microorganisms and activation of the immune response. Nature 2007, 449(7164):819-826. 10.1038/nature06246, 17943118.
20. Aderem A, Ulevitch RJ. Toll-like receptors in the induction of the innate immune response. Nature 2000, 406(6797):782-787. 10.1038/35021228, 10963608.
21. Sun L, Liu S, Chen ZJ. SnapShot: pathways of antiviral innate immunity. Cell 2010, 140(3):436-436. e432, 10.1016/j.cell.2010.01.041, 20144765.
22. Yu WC, Chan RW, Wang J, Travanty EA, Nicholls JM, Peiris JS, Mason RJ, Chan MC. Viral replication and innate host responses in primary human alveolar epithelial cells and alveolar macrophages infected with influenza H5N1 and H1N1 viruses. J Virol 2011, 85(14):6844-6855. 10.1128/JVI.02200-10, 3126566, 21543489.
23. Reading PC, Whitney PG, Pickett DL, Tate MD, Brooks AG. Influenza viruses differ in ability to infect macrophages and to induce a local inflammatory response following intraperitoneal injection of mice. Immunol Cell Biol 2010, 88(6):641-650. 10.1038/icb.2010.11, 20142836.
24. da Huang W, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 2007, 8(9):R183. 10.1186/gb-2007-8-9-r183, 2375021, 17784955.
25. Fukuyama S, Kawaoka Y. The pathogenesis of influenza virus infections: the contributions of virus and host factors. Curr Opin Immunol 2011, 23(4):481-486. 10.1016/j.coi.2011.07.016, 3163725, 21840185.
26. Chang JT. Deriving transcriptional programs and functional processes from gene expression databases. Bioinformatics 2012, 28(8):1122-1129. 10.1093/bioinformatics/bts112, 22408194.