Human gene correlation analysis (HGCA): A tool for the identification of transcriptionally co-expressed genes

BMC Research Notes

Volumn 5, Issue , 2012, Pages

  Michalopoulos, Ioannis ^a   Pavlopoulos, Georgios A ^b   Malatras, Apostolos ^a,c   Karelas, Alexandros ^a   Kostadima, Myrto Areti ^a,d   Schneider, Reinhard ^e,f   Kossida, Sophia ^a  

^a BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^b UNIVERSITY OF LEUVEN   (Belgium)

^c UNIVERSITY OF ATHENS   (Greece)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^f UNIVERSITY OF LUXEMBOURG   (Luxembourg)

Author keywords

Functional annotation; Gene annotation; Gene coexpression; Microarray analysis

Indexed keywords

DDX4 PROTEIN, HUMAN; DEAD BOX PROTEIN; HLA ANTIGEN; ISOMERASE; LIPOCALIN; METALLOTHIONEIN; PROSTAGLANDIN R2 D ISOMERASE; PROSTAGLANDIN R2 D-ISOMERASE; RIBOSOME PROTEIN;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CLUSTER ANALYSIS; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENETICS; HIGH THROUGHPUT SCREENING; HUMAN; METHODOLOGY; MOLECULAR GENETICS; PROMOTER REGION; STATISTICAL MODEL;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DEAD-BOX RNA HELICASES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HIGH-THROUGHPUT SCREENING ASSAYS; HLA ANTIGENS; HUMANS; INTRAMOLECULAR OXIDOREDUCTASES; LIPOCALINS; METALLOTHIONEIN; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; RIBOSOMAL PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84861813302     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-5-265     Document Type: Article

References (71)

1. The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis. Jen CH, Manfield IW, Michalopoulos I, Pinney JW, Willats WG, Gilmartin PM, Westhead DR, Plant J 2006 46 336 348 10.1111/j.1365-313X.2006.02681.x 16623895 (Pubitemid 43773572)
2. Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Manfield IW, Jen CH, Pinney JW, Michalopoulos I, Bradford JR, Gilmartin PM, Westhead DR, Nucleic Acids Res 2006 34 504 W509 10.1093/nar/gkl204 16845059 (Pubitemid 44529822)
3. The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. Toufighi K, Brady SM, Austin R, Ly E, Provart NJ, Plant J 2005 43 153 163 10.1111/j.1365-313X.2005.02437.x 15960624 (Pubitemid 40962743)
4. ATTED-II provides coexpressed gene networks for Arabidopsis. Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K, Nucleic Acids Res 2009 37 987 D991 10.1093/nar/gkn807 18953027
5. ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H, Nucleic Acids Res 2007 35 863 D869 10.1093/nar/gkl783 17130150 (Pubitemid 46056323)
6. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W, Plant Physiol 2004 136 2621 2632 10.1104/pp.104.046367 15375207 (Pubitemid 41071302)
7. CSB.DB: a comprehensive systems-biology database. Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J, Bioinformatics 2004 20 3647 3651 10.1093/bioinformatics/bth398 15247097 (Pubitemid 40136804)
8. Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ, Plant Cell Environ 2009 32 1633 1651 10.1111/j.1365-3040.2009.02040.x 19712066
9. A gene atlas of the mouse and human protein-encoding transcriptomes. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al. Proc Natl Acad Sci U S A 2004 101 6062 6067 10.1073/pnas.0400782101 15075390 (Pubitemid 38520528)
10. COXPRESdb: a database of coexpressed gene networks in mammals. Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K, Nucleic Acids Res 2008 36 77 D82 10.1093/nar/gkn358 17932064
11. Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Lee PD, Sladek R, Greenwood CM, Hudson TJ, Genome Res 2002 12 292 297 10.1101/gr.217802 11827948 (Pubitemid 34162995)
12. Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. Prieto C, Risueno A, Fontanillo C, De las Rivas J, PLoS One 2008 3 3911 10.1371/journal.pone.0003911 19081792
13. Coexpression analysis of human genes across many microarray data sets. Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P, Genome Res 2004 14 1085 1094 10.1101/gr.1910904 15173114 (Pubitemid 38811545)
14. Application and evaluation of automated semantic annotation of gene expression experiments. French L, Lane S, Law T, Xu L, Pavlidis P, Bioinformatics 2009 25 1543 1549 10.1093/bioinformatics/btp259 19376825
15. NCBI GEO: archive for high-throughput functional genomic data. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, et al. Nucleic Acids Res 2009 37 885 D890 10.1093/nar/gkn764 18940857
16. WGCNA: an R package for weighted correlation network analysis. Langfelder P, Horvath S, BMC Bioinformatics 2008 9 559 10.1186/1471-2105-9-559 19114008
17. Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Horvath S, Zhang B, Carlson M, Lu KV, Zhu S, Felciano RM, Laurance MF, Zhao W, Qi S, Chen Z, et al. Proc Natl Acad Sci U S A 2006 103 17402 17407 10.1073/pnas.0608396103 17090670 (Pubitemid 44788981)
18. Functional organization of the transcriptome in human brain. Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S, Geschwind DH, Nat Neurosci 2008 11 1271 1282 10.1038/nn.2207 18849986
19. A systems level analysis of transcriptional changes in Alzheimers disease and normal aging. Miller JA, Oldham MC, Geschwind DH, J Neurosci 2008 28 1410 1420 10.1523/JNEUROSCI.4098-07.2008 18256261 (Pubitemid 351231536)
20. A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility. Keller MP, Choi Y, Wang P, Davis DB, Rabaglia ME, Oler AT, Stapleton DS, Argmann C, Schueler KL, Edwards S, et al. Genome Res 2008 18 706 716 10.1101/gr.074914.107 18347327 (Pubitemid 351645061)
21. Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Oldham MC, Horvath S, Geschwind DH, Proc Natl Acad Sci U S A 2006 103 17973 17978 10.1073/pnas.0605938103 17101986 (Pubitemid 44852270)
22. Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome. Presson AP, Sobel EM, Papp JC, Suarez CJ, Whistler T, Rajeevan MS, Vernon SD, Horvath S, BMC Syst Biol 2008 2 95 10.1186/1752-0509-2-95 18986552
23. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, et al. Genome Biol 2009 10 130 10.1186/gb-2009-10-11-r130 19919682
24. Network visualization and analysis of gene expression data using BioLayout Express(3D). Theocharidis A, van Dongen S, Enright AJ, Freeman TC, Nat Protoc 2009 4 1535 1550 10.1038/nprot.2009.177 19798086
25. Loss of compartmentalization causes misregulation of lysine biosynthesis in peroxisome-deficient yeast cells. Breitling R, Sharif O, Hartman ML, Krisans SK, Eukaryot Cell 2002 1 978 986 10.1128/EC.1.6.978-986.2002 12477798 (Pubitemid 36557718)
26. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM, Cancer Res 2002 62 4427 4433 12154050 (Pubitemid 34827303)
27. Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC, Nucleic Acids Res 2002 30 48 10.1093/nar/30.10.e48 12000853
28. Repeated observation of breast tumor subtypes in independent gene expression data sets. Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, et al. Proc Natl Acad Sci U S A 2003 100 8418 8423 10.1073/pnas.0932692100 12829800 (Pubitemid 36842560)
29. A molecular signature of metastasis in primary solid tumors. Ramaswamy S, Ross KN, Lander ES, Golub TR, Nat Genet 2003 33 49 54 10.1038/ng1060 12469122 (Pubitemid 36068681)
30. Dysregulation of the annexin family protein family is associated with prostate cancer progression. Xin W, Rhodes DR, Ingold C, Chinnaiyan AM, Rubin MA, Am J Pathol 2003 162 255 261 10.1016/S0002-9440(10)63816-3 12507908 (Pubitemid 36042007)
31. Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M, Genome Res 2001 11 1463 1468 10.1101/gr.207401 11544189 (Pubitemid 32894671)
32. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC, Mol Cell 2002 9 1133 1143 10.1016/S1097- 2765(02)00531-2 12049748 (Pubitemid 34626681)
33. Comparative assessment of large-scale data sets of protein-protein interactions. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P, Nature 2002 417 399 403 12000970 (Pubitemid 34563526)
34. Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Franke L, van Bakel H, Fokkens L, de Jong ED, Egmont-Petersen M, Wijmenga C, Am J Hum Genet 2006 78 1011 1025 10.1086/504300 16685651 (Pubitemid 43787692)
35. Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. Cheng WC, Tsai ML, Chang CW, Huang CL, Chen CR, Shu WY, Lee YS, Wang TH, Hong JH, Li CY, et al. BMC Bioinformatics 2010 11 421 10.1186/1471-2105-11-421 20698961
36. Affymetrix Power Tools. http://www.affymetrix.com/partners-programs/ programs/developer/tools/powertools.affx
37. Evaluation of error detection polynomial performance on the AUTOVON channel. Brayer K, Hammond JL, IEEE National Telecommunications Conference Institute of Electrical and Electronics Engineers, New Orleans, LA 1975 8-21 to 28-25
38. Robust estimators for expression analysis. Hubbell E, Liu WM, Mei R, Bioinformatics 2002 18 1585 1592 10.1093/bioinformatics/18.12.1585 12490442 (Pubitemid 36097723)
39. Ensembl 2009. Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, et al. Nucleic Acids Res 2009 37 690 D697 10.1093/nar/gkn828 19033362
40. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000 25 25 29 10.1038/75556 10802651 (Pubitemid 30257031)
41. From genomics to chemical genomics: new developments in KEGG. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M, Nucleic Acids Res 2006 34 354 D357 10.1093/nar/gkj102 16381885
42. InterPro: the integrative protein signature database. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al. Nucleic Acids Res 2009 37 211 D215 10.1093/nar/gkn785 18940856
43. Online Mendelian Inheritance in Man (OMIM) as a knowledgebase for human developmental disorders. Boyadjiev SA, Jabs EW, Clin Genet 2000 57 253 266 10845565
44. Online Mendelian Inheritance in Man (OMIM). Hamosh A, Scott AF, Amberger J, Valle D, McKusick VA, Hum Mutat 2000 15 57 61 10.1002/(SICI)1098-1004(200001) 15:1<57::AID-HUMU12>3.0.CO;2-G 10612823 (Pubitemid 30036170)
45. TRANSFAC: transcriptional regulation, from patterns to profiles. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, et al. Nucleic Acids Res 2003 31 374 378 10.1093/nar/gkg108 12520026 (Pubitemid 36150406)
46. MATCH: A tool for searching transcription factor binding sites in DNA sequences. Kel AE, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E, Nucleic Acids Res 2003 31 3576 3579 10.1093/nar/gkg585 12824369 (Pubitemid 37442201)
47. Thirteen Ways to Look at the Correlation Coefficient. Rodgers JL, Nicewander WA, Am Stat 1988 42 59 66
48. Kendall M, Stuart A, Ord J, The Advanced Theory of Statistics Charles Griffin, London 4 1977
49. Shannon CE, Weaver W, The Mathematical Theory of Communication University of Illinois Press, Urbana, IL 1949
50. Il calcolo delle assicurazioni su gruppi di teste. Bonferroni CE, Studi in Onore del Professore Salvatore Ortu Carboni Rome, Italy 1935 13 60
51. Distance matrix programs. http://evolution.genetics.washington.edu/ phylip/doc/distance.html
52. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Saitou N, Nei M, Mol Biol Evol 1987 4 406 425 3447015
53. Why Neighbor-Joining Works. Mihaescu R, Levy D, Pachter L, Algorithmica 2009 54 1 24 10.1007/s00453-007-9116-4
54. QuickJoin-fast neighbour-joining tree reconstruction. Mailund T, Pedersen CN, Bioinformatics 2004 20 3261 3262 10.1093/bioinformatics/bth359 15201185 (Pubitemid 39619222)
55. A reference guide for tree analysis and visualization. Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R, BioData Min 2010 3 1 10.1186/1756-0381-3-1 20175922
56. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Benjamini Y, Hochberg Y, J Roy Statist Soc Ser B 1995 57 289 300
57. The tail of the hypergeometric distribution. Chvátal V, Discrete Math 1979 25 285 287 10.1016/0012-365X(79)90084-0
58. Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. Ihmels J, Bergmann S, Berman J, Barkai N, PLoS Genet 2005 1 39 10.1371/journal.pgen.0010039 16470937
59. Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Tanay A, Regev A, Shamir R, Proc Natl Acad Sci U S A 2005 102 7203 7208 10.1073/pnas.0502521102 15883364 (Pubitemid 40696358)
60. Metallothionein induction by hypoxia involves cooperative interactions between metal-responsive transcription factor-1 and hypoxia-inducible transcription factor-1alpha. Murphy BJ, Kimura T, Sato BG, Shi Y, Andrews GK, Mol Cancer Res 2008 6 483 490 10.1158/1541-7786.MCR-07-0341 18337454 (Pubitemid 351416538)
61. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, et al. Nucleic Acids Res 2011 39 561 D568 10.1093/nar/gkq973 21045058
62. The biology of hair follicles. Paus R, Cotsarelis G, N Engl J Med 1999 341 491 497 10.1056/NEJM199908123410706 10441606 (Pubitemid 29372890)
63. Prostaglandin d2 inhibits hair growth and is elevated in bald scalp of men with androgenetic alopecia. Garza LA, Liu Y, Yang Z, Alagesan B, Lawson JA, Norberg SM, Loy DE, Zhao T, Blatt HB, Stanton DC, et al. Sci Transl Med 2012 4 126 134
64. Sox10 gain-of-function causes XX sex reversal in mice: implications for human 22q-linked disorders of sex development. Polanco JC, Wilhelm D, Davidson TL, Knight D, Koopman P, Hum Mol Genet 2010 19 506 516 10.1093/hmg/ddp520 19933217
65. Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Kuramochi-Miyagawa S, Kimura T, Ijiri TW, Isobe T, Asada N, Fujita Y, Ikawa M, Iwai N, Okabe M, Deng W, et al. Development 2004 131 839 849 10.1242/dev.00973 14736746 (Pubitemid 38263199)
66. Mouse MAELSTROM: the link between meiotic silencing of unsynapsed chromatin and microRNA pathway? Costa Y, Speed RM, Gautier P, Semple CA, Maratou K, Turner JM, Cooke HJ, Hum Mol Genet 2006 15 2324 2334 10.1093/hmg/ddl158 16787967 (Pubitemid 44288678)
67. Relative efficiencies of the fitch-margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Saitou N, Imanishi T, Mol Biol Evol 1989 6 514 525
68. Dendroscope: An interactive viewer for large phylogenetic trees. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R, BMC Bioinformatics 2007 8 460 10.1186/1471-2105-8-460 18034891 (Pubitemid 351168201)
69. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Letunic I, Bork P, Bioinformatics 2007 23 127 128 10.1093/bioinformatics/btl529 17050570 (Pubitemid 46017867)
70. Construction, visualisation, and clustering of transcription networks from microarray expression data. Freeman TC, Goldovsky L, Brosch M, van Dongen S, Maziere P, Grocock RJ, Freilich S, Thornton J, Enright AJ, PLoS Comp Biol 2007 3 2032 2042 (Pubitemid 350043416)
71. An efficient algorithm for large-scale detection of protein families. Enright AJ, Van Dongen S, Ouzounis CA, Nucleic Acids Res 2002 30 1575 1584 10.1093/nar/30.7.1575 11917018 (Pubitemid 34679732)