Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome Stability

PLoS Computational Biology

Volumn 8, Issue 8, 2012, Pages

  Zhang, Jie ^a,b   Lu, Kewei ^a   Xiang, Yang ^a   Islam, Muhtadi ^a   Kotian, Shweta ^a   Kais, Zeina ^a   Lee, Cindy ^a   Arora, Mansi ^a   Liu, Hui wen ^a   Parvin, Jeffrey D ^a,b   Huang, Kun ^a,b  

^a OHIO STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA MINING; DISEASES; TISSUE;

CO-EXPRESSION NETWORKS; DISEASE BIOMARKER; EXPRESSED GENES; GENE FUNCTION; GENOME STABILITY; MICROARRAY DATASET; MINING ALGORITHMS; MOLECULAR DEVELOPMENT; MOLECULAR ORIGINS; NORMAL TISSUE;

GENE EXPRESSION;

ALGORITHM; ARTICLE; BREAST CANCER; CANCER PROGNOSIS; CENTROSOME; DATA MINING; DNA REPAIR; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENOMIC INSTABILITY; GLIOBLASTOMA; MARKER GENE; MKI67 GENE; OVARY CANCER; QUASI CLIQUE MERGER ALGORITHM; RNA INTERFERENCE; TRANSCRIPTOMICS;

EID: 84866065824     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002656     Document Type: Article

References (78)

1. Van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415: 530-536.
2. Van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347: 1999-2009.
3. Buyse M, Loi S, van't Veer L, Viale G, Delorenzi M, et al. (2006) Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 98: 1183-1192.
4. Hu H, Yan X, Huang Y, Han J, Zhou XJ, (2005) Mining coherent dense subgraphs across massive biological networks for functional discovery. Bioinformatics 21 Suppl 1: i213-221.
5. Pujana MA, Han JD, Starita LM, Stevens KN, Tewari M, et al. (2007) Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 39: 1338-1349.
6. Langfelder P, Horvath S, (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9: 559.
7. Horvath S, Zhang B, Carlson M, Lu KV, Zhu S, et al. (2006) Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A 103: 17402-17407.
8. Li H, Sun Y, Zhan M, (2009) Exploring pathways from gene co-expression to network dynamics. Methods Mol Biol 541: 249-267.
9. Zhang J, Xiang Y, Jin R, Huang K (2009) Using frequent co-expression network to identify gene clusters for breast cancer prognosis. In: Proceedings of the ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing; 3-5 August 2009; Shanghai, China. Available: http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=05260407. Accessed 17 July 2012.
10. Zhang B, Horvath S, (2005) A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4: Article17.
11. Kais Z, Barsky SH, Mathsyaraja H, Zha A, Ransburgh DJ, et al. (2011) KIAA0101 interacts with BRCA1 and regulates centrosome number. Mol Cancer Res 9: 1091-9.
12. Langfelder P, Horvath S, (2007) Eigengene networks for studying the relationships between co- expression modules. BMC Syst Biol 1: 54.
13. Li A, Horvath S, (2009) Network module detection: Affinity search technique with the multi-node topological overlap measure. BMC Res Notes 2: 142.
14. MacLennan NK, Dong J, Aten JE, Horvath S, Rahib L, et al. (2009) Weighted gene co-expression network analysis identifies biomarkers in glycerol kinase deficient mice. Mol Genet Metab 98: 203-214.
15. Yip AM, Horvath S, (2007) Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics 8: 22.
16. Ou Y, Cun-Quan Zhang, (2007) A new multimembership clustering method. J Ind Manag Optim 3: 619-624.
17. James Abello MGCR, Sandra Sudarsky (2002) Massive quasi-clique detection. In: Proceedings of the 5th Latin American Symposium on Theoretical Informatics; 3-6 April, 2002; Cancun, Mexico. Available: http://www.springerlink.com/content/978-3-540-43400-9/. Accessed 17 July 2012.
18. Seidman SB, (1983) Network structure and minimum degree. Soc Networks 5: 269-287.
19. Minguez P, Dopazo J, (2011) Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties. PLoS One 6: e17474.
20. Ein-Dor L, Kela I, Getz G, Givol D, Domany E, (2005) Outcome signature genes in breast cancer: is there a unique set? Bioinformatics 21: 171-178.
21. Oldham MC, Horvath S, Geschwind DH, (2006) Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci U S A 103: 17973-17978.
22. Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, et al. (2006) Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 98: 262-272.
23. Dai H, van't Veer L, Lamb J, He YD, Mao M, et al. (2005) A cell proliferation signature is a marker of extremely poor outcome in a subpopulation of breast cancer patients. Cancer Res 65: 4059-4066.
24. Ivshina AV, George J, Senko O, Mow B, Putti TC, et al. (2006) Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res 66: 10292-10301.
25. Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z, (2006) A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet 38: 1043-1048.
26. Lee JS, Chu IS, Heo J, Calvisi DF, Sun Z, et al. (2004) Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling. Hepatology 40: 667-676.
27. Stuart JE, Lusis EA, Scheck AC, Coons SW, Lal A, et al. (2011) Identification of gene markers associated with aggressive meningioma by filtering across multiple sets of gene expression arrays. J Neuropathol Exp Neurol 70: 1-12.
28. Zhang J, Liu B, Jiang X, Zhao H, Fan M, et al. (2009) A systems biology-based gene expression classifier of glioblastoma predicts survival with solid tumors. PLoS One 4: e6274.
29. Ziche M, Maglione D, Ribatti D, Morbidelli L, Lago CT, et al. (1997) Placenta growth factor-1 is chemotactic, mitogenic, and angiogenic. Lab Invest 76: 517-531.
30. Shyu KG, Hung HF, Wang BW, Chang H, (2008) Hyperbaric oxygen induces placental growth factor expression in bone marrow-derived mesenchymal stem cells. Life Sci 83: 65-73.
31. Tan BC, Lee SC, (2004) Nek9, a novel FACT-associated protein, modulates interphase progression. J Biol Chem 279: 9321-9330.
32. Lawo S, Bashkurov M, Mullin M, Ferreria MG, Kittler R, et al. (2009) HAUS, the 8 subunit human Augmin complex, regulates centrosome and spindle integrity. Curr Biol 19: 816-826.
33. King MC, Marks JH, Mandell JB, (2003) Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science 302: 643-646.
34. Konstantinopoulos PA, Cannistra SA, Fountzilas H, Culhane A, Pillay K, et al. (2011) Integrated analysis of multiple microarray datasets identifies a reproducible survival predictor in ovarian cancer. PLoS One 6: e18202.
35. Lengauer C, Kinzler KW, Vogelstein B, (1998) Genetic instabilities in human cancers. Nature 396: 643-649.
36. Pihan GA, Purohit A, Wallace J, Knecht H, Woda B, et al. (1998) Centrosome defects and genetic instability in malignant tumors. Cancer Res 58: 3974-3985.
37. Sankaran S, Starita LM, Simons AM, Parvin JD, (2006) Identification of domains of BRCA1 critical for the ubiquitin-dependent inhibition of centrosome function. Cancer Res 66: 4100-4107.
38. Bourke E, Dodson H, Merdes A, Cuffe L, Zachos G, et al. (2007) DNA damage induces Chk1- dependent centrosome amplification. EMBO Rep 8: 603-609.
39. Griffith E, Walker S, Martin CA, Vagnarelli P, Stiff T, et al. (2008) Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling. Nat Genet 40: 232-236.
40. Joukov V, Groen AC, Prokhorova T, Gerson R, White E, et al. (2006) The BRCA1/BARD1 heterodimer modulates ran-dependent mitotic spindle assembly. Cell 127: 539-552.
41. Nakanishi A, Han X, Saito H, Taguchi K, Ohta Y, et al. (2007) Interference with BRCA2, which localizes to the centrosome during S and early M phase, leads to abnormal nuclear division. Biochem Biophys Res Commun 355: 34-40.
42. Parvin J, Chiba N, Ransburgh D, (2011) Identifying the Effects of BRCA1 Mutations on Homologous Recombination using Cells that Express Endogenous Wild-type BRCA1. J Vis Exp doi: 10.3791/2468.
43. Moynahan ME, Chiu JW, Koller BH, Jasin M, (1999) Brca1 controls homology-directed DNA repair. Mol Cell 4: 511-518.
44. Xu X, Weaver Z, Linke SP, Li C, Gotay J, et al. (1999) Centrosome amplification and a defective G2-M cell cycle checkpoint induce genetic instability in BRCA1 exon 11 isoform-deficient cells. Mol Cell 3: 389-395.
45. Starita LM, Machida Y, Sankaran S, Elias JE, Griffin K, et al. (2004) BRCA1-dependent ubiquitination of gamma-tubulin regulates centrosome number. Mol Cell Biol 24: 8457-8466.
46. Laufer M, Nandula SV, Modi AP, Wang S, Jasin M, et al. (2007) Structural requirements for the BARD1 tumor suppressor in chromosomal stability and homology-directed DNA repair. J Biol Chem 282: 34325-34333.
47. Wu L, Hickson ID, (2003) The Bloom's syndrome helicase suppresses crossing over during homologous recombination. Nature 426: 870-874.
48. Plank JL, Wu J, Hsieh TS, (2006) Topoisomerase IIIalpha and Bloom's helicase can resolve a mobile double Holliday junction substrate through convergent branch migration. Proc Natl Acad Sci U S A 103: 11118-11123.
49. Emanuele MJ, Ciccia A, Elia AE, Elledge SJ, (2011) Proliferating cell nuclear antigen (PCNA)- associated KIAA0101/PAF15 protein is a cell cycle-regulated anaphase-promoting complex/cyclosome substrate. Proc Natl Acad Sci U S A 108: 9845-9850.
50. Umehara T, Horikoshi M, (2003) Transcription initiation factor IID-interactive histone chaperone CIA-II implicated in mammalian spermatogenesis. J Biol Chem 278: 35660-35667.
51. Mello JA, Sillje HH, Roche DM, Kirschner DB, Nigg EA, et al. (2002) Human Asf1 and CAF-1 interact and synergize in a repair-coupled nucleosome assembly pathway. EMBO Rep 3: 329-334.
52. Tagami H, Ray-Gallet D, Almouzni G, Nakatani Y, (2004) Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116: 51-61.
53. Tamburini BA, Carson JJ, Adkins MW, Tyler JK, (2005) Functional conservation and specialization among eukaryotic anti-silencing function 1 histone chaperones. Eukaryot Cell 4: 1583-1590.
54. Groth A, Ray-Gallet D, Quivy JP, Lukas J, Bartek J, et al. (2005) Human Asf1 regulates the flow of S phase histones during replicational stress. Mol Cell 17: 301-311.
55. Laprise P, Viel A, Rivard N, (2004) Human homolog of disc-large is required for adherens junction assembly and differentiation of human intestinal epithelial cells. J Biol Chem 279: 10157-10166.
56. Tsou AP, Yang CW, Huang CY, Yu RC, Lee YC, et al. (2003) Identification of a novel cell cycle regulated gene, HURP, overexpressed in human hepatocellular carcinoma. Oncogene 22: 298-307.
57. Wang H, Hu X, Ding X, Dou Z, Yang Z, et al. (2004) Human Zwint-1 specifies localization of Zeste White 10 to kinetochores and is essential for mitotic checkpoint signaling. J Biol Chem 279: 54590-54598.
58. Musio A, Mariani T, Montagna C, Zambroni D, Ascoli C, et al. (2004) Recapitulation of the Roberts syndrome cellular phenotype by inhibition of INCENP, ZWINT-1 and ZW10 genes. Gene 331: 33-40.
59. Yerushalmi R, Woods R, Ravdin PM, Hayes MM, Gelmon KA, (2010) Ki67 in breast cancer: prognostic and predictive potential. Lancet Oncol 11: 174-183.
60. Gruneberg U, Neef R, Li X, Chan EH, Chalamalasetty RB, et al. (2006) KIF14 and citron kinase act together to promote efficient cytokinesis. J Cell Biol 172: 363-372.
61. Carleton M, Mao M, Biery M, Warrener P, Kim S, et al. (2006) RNA interference-mediated silencing of mitotic kinesin KIF14 disrupts cell cycle progression and induces cytokinesis failure. Mol Cell Biol 26: 3853-3863.
62. Theriault BL, Pajovic S, Bernardini MQ, Shaw PA, Gallie BL, (2012) Kinesin family member 14: An independent prognostic marker and potential therapeutic target for ovarian cancer. Int J Cancer 130: 1844-54.
63. Valk K, Vooder T, Kolde R, Reintam MA, Petzold C, et al. (2010) Gene expression profiles of non- small cell lung cancer: survival prediction and new biomarkers. Oncology 79: 283-292.
64. Hanahan D, Weinberg RA, (2000) The hallmarks of cancer. Cell 100: 57-70.
65. Hanahan D, Weinberg RA, (2011) Hallmarks of cancer: the next generation. Cell 144: 646-674.
66. Kostka D, Spang R, (2004) Finding disease specific alterations in the co-expression of genes. Bioinformatics 20 Suppl 1: i194-199.
67. Choi JK, Yu U, Yoo OJ, Kim S, (2005) Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21: 4348-4355.
68. Cho SB, Kim J, Kim JH, (2009) Identifying set-wise differential co-expression in gene expression microarray data. BMC Bioinformatics 10: 109.
69. Weaver BA, Cleveland DW, (2009) The role of aneuploidy in promoting and suppressing tumors. J Cell Biol 185: 935-937.
70. Kops GJ, Weaver BA, Cleveland DW, (2005) On the road to cancer: aneuploidy and the mitotic checkpoint. Nat Rev Cancer 5: 773-785.
71. Damasco C, Lembo A, Somma MP, Gatti M, Di Cunto F, et al. (2011) A signature inferred from Drosophila mitotic genes predicts survival of breast cancer patients. PLoS One 6: e14737.
72. Somma MP, Ceprani F, Bucciarelli E, Naim V, De Arcangelis V, et al. (2008) Identification of Drosophila mitotic genes by combining co-expression analysis and RNA interference. PLoS Genet 4: e1000126.
73. Asteriti IA, Rensen WM, Lindon C, Lavia P, Guarguaglini G, (2010) The Aurora-A/TPX2 complex: a novel oncogenic holoenzyme? Biochim Biophys Acta 1806: 230-239.
74. Karthigeyan D, Prasad SB, Shandilya J, Agrawal S, Kundu TK, (2010) Biology of Aurora A kinase: Implications in cancer manifestation and therapy. Med Res Rev E-pub ahead of print.
75. Ransburgh DJ, Chiba N, Ishioka C, Toland AE, Parvin JD, (2010) Identification of breast tumor mutations in BRCA1 that abolish its function in homologous DNA recombination. Cancer Res 70: 988-995.
76. D'Assoro AB, Stivala F, Barrett S, Ferrigno G, Salisbury JL, (2001) GFP-centrin as a marker for centriole dynamics in the human breast cancer cell line MCF-7. Ital J Anat Embryol 106: 103-110.
77. Efron B, (1988) Logistic Regression, Survival Analysis, and the Kaplan-Meier Curve. J Am Stat Assoc 83: 414-425.
78. Wu J, Vallenius T, Ovaska K, Westermarck J, Makela TP, et al. (2009) Integrated network analysis platform for protein-protein interactions. Nat Methods 6: 75-77.