Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition

Epigenetics and Chromatin

Volumn 6, Issue 1, 2013, Pages

  Cieślik, Marcin ^a   Hoang, Stephen A ^a   Baranova, Natalya ^a   Chodaparambil, Sanjay ^a   Kumar, Manish ^a   Allison, David F ^a   Xu, Xiaojiang ^a   Wamsley, J Jacob ^a   Gray, Lisa ^a   Jones, David R ^a   Mayo, Marty W ^a   Bekiranov, Stefan ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

Author keywords

Chromatin; EMT; Epigenetics; Feedback; Reprogramming

Indexed keywords

I KAPPA B;

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; CONTROLLED STUDY; DEREGULATION; DNA METHYLATION; ENHANCER REGION; ENZYME ACTIVITY; EPIGENETICS; EPITHELIAL MESENCHYMAL TRANSITION; FEEDBACK SYSTEM; GENE LOCUS; HISTONE MODIFICATION; HUMAN; HUMAN CELL; HYPOTHESIS; LUNG NON SMALL CELL CANCER; NUCLEAR REPROGRAMMING; POSITIVE FEEDBACK; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; UPREGULATION;

EID: 84883157168     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-6-28     Document Type: Article

References (91)

1. Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo. Arnold SJ, Robertson EJ, Nat Rev Mol Cell Biol 2009 10 91 103 10.1038/nrm2618 19129791
2. The basics of epithelial-mesenchymal transition. Kalluri R, Weinberg RA, J Clin Invest 2009 119 1420 1428 10.1172/JCI39104 19487818
3. Epithelial-mesenchymal transitions in development and pathologies. Thiery JP, Curr Opin Cell Biol 2003 15 740 746 10.1016/j.ceb.2003.10.006 14644200 (Pubitemid 37487967)
4. Epithelial-mesenchymal transition: at the crossroads of development and tumor metastasis. Yang J, Weinberg RA, Dev Cell 2008 14 818 829 10.1016/j.devcel.2008.05.009 18539112 (Pubitemid 351757205)
5. Epithelial-mesenchymal transitions in development and disease. Thiery JP, Acloque H, Huang RYJ, Nieto MA, Cell 2009 139 871 890 10.1016/j.cell.2009.11. 007 19945376
6. The epithelial-mesenchymal transition generates cells with properties of stem cells. Mani SA, Guo W, Liao M-J, Eaton EN, Ayyanan A, Zhou AY, Brooks M, Reinhard F, Zhang CC, Shipitsin M, Campbell LL, Polyak K, Brisken C, Yang J, Weinberg RA, Cell 2008 133 704 715 10.1016/j.cell.2008.03.027 18485877 (Pubitemid 351636299)
7. Epithelial to mesenchymal transition is a determinant of sensitivity of non-small-cell lung carcinoma cell lines and xenografts to epidermal growth factor receptor inhibition. Thomson S, Buck E, Petti F, Griffin G, Brown E, Ramnarine N, Iwata KK, Gibson N, Haley JD, Cancer Res 2005 65 9455 10.1158/0008-5472.CAN-05-1058 16230409 (Pubitemid 41508014)
8. EMT, cancer stem cells and drug resistance: an emerging axis of evil in the war on cancer. Singh A, Settleman J, Oncogene 2010 29 4741 4751 10.1038/onc.2010.215 20531305
9. Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition. McDonald OG, Wu H, Timp W, Doi A, Feinberg AP, Nat Struct Mol Biol 2011 18 867 874 10.1038/nsmb.2084 21725293
10. Sustained induction of epithelial to mesenchymal transition activates DNA methylation of genes silenced in basal-like breast cancers. Dumont N, Wilson MB, Crawford YG, Reynolds PA, Sigaroudinia M, Tlsty TD, Proc Natl Acad Sci 2008 105 14867 14872 10.1073/pnas.0807146105 18806226
11. E-cadherin transcriptional downregulation by promoter methylation but not mutation is related to epithelial-to-mesenchymal transition in breast cancer cell lines. Lombaerts M, van Wezel T, Philippo K, Dierssen JWF, Zimmerman RME, Oosting J, van Eijk R, Eilers PH, van de Water B, Cornelisse CJ, Cleton-Jansen A-M, Br J Cancer 2006 94 661 671 16495925 (Pubitemid 43361897)
12. The language of covalent histone modifications. Strahl BD, Allis CD, Nature 2000 403 41 45 10.1038/47412 10638745 (Pubitemid 30038513)
13. Histone and chromatin cross-talk. Fischle W, Wang Y, Allis CD, Curr Opin Cell Biol 2003 15 172 183 10.1016/S0955-0674(03)00013-9 12648673 (Pubitemid 36332192)
14. DNA methylation patterns and epigenetic memory. Bird A, Genes Dev 2002 16 6 21 10.1101/gad.947102 11782440 (Pubitemid 34049633)
15. A systems view of epithelial-mesenchymal transition signaling states. Thomson S, Petti F, Sujka-Kwok I, Mercado P, Bean J, Monaghan M, Seymour SL, Argast GM, Epstein DM, Haley JD, Clin Exp Metastasis 2011 28 137 155 10.1007/s10585-010-9367-3 21194007
16. Discovery and characterization of chromatin states for systematic annotation of the human genome. Ernst J, Kellis M, Nat Biotech 2010 28 817 825 10.1038/nbt.1662
17. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE, Nature 2011 473 43 49 10.1038/nature09906 21441907
18. Enhancer function: new insights into the regulation of tissue-specific gene expression. Ong C-T, Corces VG, Nat Rev Genet 2011 12 283 293 21358745
19. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SCR, Kuroda MI, Pirrotta V, Karpen GH, Park PJ, Nature 2011 471 480 485 10.1038/nature09725 21179089
20. High-resolution mapping and characterization of open chromatin across the genome. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE, Cell 2008 132 311 322 10.1016/j.cell.2007.12.014 18243105 (Pubitemid 351172431)
21. Distinctive chromatin in human sperm packages genes for embryo development. Hammoud SS, Nix DA, Zhang H, Purwar J, Carrell DT, Cairns BR, Nature 2009 460 473 478 19525931
22. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Zentner GE, Tesar PJ, Scacheri PC, Genome Res 2011 21 1273 1283 10.1101/gr.122382.111 21632746
23. Multilineage priming of enhancer repertoires precedes commitment to the b and myeloid cell lineages in hematopoietic progenitors. Mercer EM, Lin YC, Benner C, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C, Immunity 2011 35 413 425 10.1016/j.immuni.2011.06.013 21903424
24. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo Q-M, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Ren B, Cell Res 2011 21 1393 1409 10.1038/cr.2011.146 21876557
25. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R, Proc Natl Acad Sci USA 2010 107 21931 21936 10.1073/pnas.1016071107 21106759
26. A continuous tumor-cell line from a human lung carcinoma with properties of type II alveolar epithelial cells. Lieber M, Smith B, Szakal A, Nelson-Rees W, Todaro G, Int J Cancer J Int Cancer 1976 17 62 70 10.1002/ijc.2910170110
27. Transforming growth factor-β1 (TGF-β1) driven epithelial to mesenchymal transition (EMT) is accentuated by tumour necrosis factor α (TNFα) via crosstalk between the SMAD and NF-κB pathways. Borthwick LA, Gardner A, Soyza AD, Mann DA, Fisher AJ, Cancer Microenviron 2012 5 45 57 10.1007/s12307-011-0080-9 21792635
28. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh T-Y, Watford WT, Schones DE, Peng W, Sun H-W, Paul WE, O'Shea JJ, Zhao K, Immunity 2009 30 155 167 10.1016/j.immuni.2008.12.009 19144320
29. Differential chromatin marking of introns and expressed exons by H3K36me3. Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J, Nat Genet 2009 41 376 381 10.1038/ng.322 19182803
30. High-resolution profiling of histone methylations in the human genome. Barski A, Cuddapah S, Cui K, Roh T-Y, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K, Cell 2007 129 823 837 10.1016/j.cell.2007.05.009 17512414 (Pubitemid 46802390)
31. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B, Nature 2009 459 108 112 10.1038/nature07829 19295514
32. Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression. Xu X, Hoang S, Mayo M, Bekiranov S, BMC Bioinforma 2010 11 396
33. AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. Newman A, Cooper J, BMC Bioinforma 2010 11 117 10.1186/1471-2105-11-117
34. Quantification of histone modification ChIP-seq enrichment for data mining and machine learning applications. Hoang SA, Xu X, Bekiranov S, Bmc Res Notes 2011 4 288 10.1186/1756-0500-4-288 21834981
35. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, Zhao K, Cell 2009 138 1019 1031 10.1016/j.cell.2009.06.049 19698979
36. Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. Wang Y, Zhang X-S, Xia Y, Nucleic Acids Res 2009 37 5943 5958 10.1093/nar/gkp625 19661283
37. Molecular signatures database (MSigDB) 3.0. Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov JP, Bioinformatics 2011 27 1739 1740 10.1093/bioinformatics/btr260 21546393
38. Gene expression profiling of breast cell lines identifies potential new basal markers. Charafe-Jauffret E, Ginestier C, Monville F, Finetti P, Adélaïde J, Cervera N, Fekairi S, Xerri L, Jacquemier J, Birnbaum D, Bertucci F, Oncogene 2006 25 2273 2284 10.1038/sj.onc.1209254 16288205
39. Zonal heterogeneity for gene expression in human pancreatic carcinoma. Nakamura T, Kuwai T, Kitadai Y, Sasaki T, Fan D, Coombes KR, Kim S-J, Fidler IJ, Cancer Res 2007 67 7597 7604 10.1158/0008-5472.CAN-07-0874 17699763 (Pubitemid 47281351)
40. Global alterations in mRNA polysomal recruitment in a cell model of colorectal cancer progression to metastasis. Provenzani A, Fronza R, Loreni F, Pascale A, Amadio M, Quattrone A, Carcinogenesis 2006 27 1323 1333 10.1093/carcin/bgi377 16531451 (Pubitemid 43985407)
41. Feedback regulation of EGFR signalling: decision making by early and delayed loops. Avraham R, Yarden Y, Nat Rev Mol Cell Biol 2011 12 104 117 10.1038/nrm3048 21252999
42. Beta-Arrestin inhibits NF-kappaB activity by means of its interaction with the NF-kappaB inhibitor IkappaBalpha. Witherow DS, Garrison TR, Miller WE, Lefkowitz RJ, Proc Natl Acad Sci USA 2004 101 8603 8607 10.1073/pnas.0402851101 15173580 (Pubitemid 38745817)
43. Arrestin development: emerging roles for β-arrestins in developmental signaling pathways. Kovacs JJ, Hara MR, Davenport CL, Kim J, Lefkowitz RJ, Dev Cell 2009 17 443 458 10.1016/j.devcel.2009.09.011 19853559
44. The clinical significance of β-arrestin 2 expression in the serum of non-small cell lung cancer patients. Wu Z, Tong W, Tan Z, Wang S, Lin P, Zhongguo Fei Ai Za Zhi Chin J Lung Cancer 2011 14 497 501
45. Triple-negative breast cancer. Foulkes WD, Smith IE, Reis-Filho JS, N Engl J Med 2010 363 1938 1948 10.1056/NEJMra1001389 21067385
46. An epithelial-mesenchymal transition (EMT) gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Byers LA, Diao L, Wang J, Saintigny P, Girard L, Peyton M, Shen L, Fan Y-H, Giri U, Tumula P, Nilsson MB, Gudikote J, Tran HT, Cardnell RJ, Bearss DJ, Warner SL, Foulks JM, Kanner SB, Gandhi V, Krett NL, Rosen ST, Kim ES, Herbst RS, Blumenschein GR, Lee JJ, Lippman SM, Ang K-K, Mills GB, Hong WK, Weinstein JN, et al. Clin Cancer Res 2012 19 279 290 23091115
47. TGF-beta1 induces human alveolar epithelial to mesenchymal cell transition (EMT). Kasai H, Allen JT, Mason RM, Kamimura T, Zhang Z, Respir Res 2005 6 56 10.1186/1465-9921-6-56 15946381 (Pubitemid 41410179)
48. TNF-α/NF-κB/Snail pathway in cancer cell migration and invasion. Wu Y, Zhou BP, Br J Cancer 2010 102 639 644 10.1038/sj.bjc.6605530 20087353
49. TGF-β inhibition enhances chemotherapy action against triple-negative breast cancer. Bhola NE, Balko JM, Dugger TC, Kuba MG, Sánchez V, Sanders M, Stanford J, Cook RS, Arteaga CL, J Clin Invest 2013 123 1348 1358 10.1172/JCI65416 23391723
50. ChIP-seq accurately predicts tissue-specific activity of enhancers. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA, Nature 2009 457 854 858 10.1038/nature07730 19212405
51. Large-scale discovery of enhancers from human heart tissue. May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Afzal V, Simpson PC, Rubin EM, Black BL, Bristow J, Pennacchio LA, Visel A, Nat Genet 2012 44 89 93
52. GREAT improves functional interpretation of cis-regulatory regions. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G, Nat Biotech 2010 28 495 501 10.1038/nbt.1630
53. Divergent gene regulation and growth effects by NF-kappa B in epithelial and mesenchymal cells of human skin. Hinata K, Gervin AM, Jennifer Zhang Y, Khavari PA, Oncogene 2003 22 1955 1964 10.1038/sj.onc.1206198 12673201 (Pubitemid 36523633)
54. Introduction to NF-κB: players, pathways, perspectives. Gilmore TD, Oncogene 2006 25 6680 6684 10.1038/sj.onc.1209954 17072321 (Pubitemid 44657845)
55. c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells. Nie Z, Hu G, Wei G, Cui K, Yamane A, Resch W, Wang R, Green DR, Tessarollo L, Casellas R, Zhao K, Levens D, Cell 2012 151 68 79 10.1016/j.cell.2012.08.033 23021216
56. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Ben-Porath I, Thomson MW, Carey VJ, Ge R, Bell GW, Regev A, Weinberg RA, Nat Genet 2008 40 499 507 10.1038/ng.127 18443585 (Pubitemid 351601215)
57. An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets. Zeller KI, Jegga AG, Aronow BJ, O'Donnell KA, Dang CV, Genome Biol 2003 4 69 10.1186/gb-2003-4-10-r69 14519204
58. Error and attack tolerance of complex networks. Albert R, Jeong H, Barabasi AL, Nature 2000 406 378 382 10.1038/35019019 10935628 (Pubitemid 30625551)
59. The PageRank Citation Ranking: Bringing Order to the Web. Page L, Brin S, Motwani R, Winograd T, http://ilpubs.stanford.edu:8090/422/
60. Inflammation and EMT: an alliance towards organ fibrosis and cancer progression. López-Novoa JM, Nieto MA, EMBO Mol Med 2009 1 303 314 10.1002/emmm.200900043 20049734
61. NF-κB represses E-cadherin expression and enhances epithelial to mesenchymal transition of mammary epithelial cells: potential involvement of ZEB-1 and ZEB-2. Chua HL, Bhat-Nakshatri P, Clare SE, Morimiya A, Badve S, Nakshatri H, Oncogene 2007 26 711 724 10.1038/sj.onc.1209808 16862183 (Pubitemid 46204250)
62. Combination of the pro-inflammatory cytokines IL-1, TNF-α and IL-17 leads to enhanced expression and additional recruitment of AP-1 family members, Egr-1 and NF-κB in osteoblast-like cells. Granet C, Miossec P, Cytokine 2004 26 169 177 10.1016/j.cyto.2004.03.002 15149634 (Pubitemid 38624630)
63. A module of negative feedback regulators defines growth factor signaling. Amit I, Citri A, Shay T, Lu Y, Katz M, Zhang F, Tarcic G, Siwak D, Lahad J, Jacob-Hirsch J, Amariglio N, Vaisman N, Segal E, Rechavi G, Alon U, Mills GB, Domany E, Yarden Y, Nat Genet 2007 39 503 512 10.1038/ng1987 17322878 (Pubitemid 46514770)
64. Linking epithelial-to-mesenchymal-transition and epigenetic modifications. Stadler SC, Allis CD, Semin Cancer Biol 2012 22 404 410 10.1016/j.semcancer.2012.06.007 22706095
65. Epigenetic reprogramming and post-transcriptional regulation during the epithelial-mesenchymal transition. Wu C-Y, Tsai Y-P, Wu M-Z, Teng S-C, Wu K-J, Trends Genet 2012 28 454 463 10.1016/j.tig.2012.05.005 22717049
66. E-cadherin regulates metastasis of pancreatic cancer in vivo and is suppressed by a SNAIL/HDAC1/HDAC2 repressor complex. Von Burstin J, Eser S, Paul MC, Seidler B, Brandl M, Messer M, von Werder A, Schmidt A, Mages J, Pagel P, Schnieke A, Schmid RM, Schneider G, Saur D, Gastroenterology 2009 137 361 371 371. e1-5 10.1053/j.gastro.2009.04.004 19362090
67. Kinase switching in mesenchymal-like non-small cell lung cancer lines contributes to EGFR inhibitor resistance through pathway redundancy. Thomson S, Petti F, Sujka-Kwok I, Epstein D, Haley JD, Clin Exp Metastasis 2008 25 843 854 10.1007/s10585-008-9200-4 18696232
68. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. John S, Sabo PJ, Thurman RE, Sung M-H, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA, Nat Genet 2011 43 264 268 10.1038/ng.759 21258342
69. PU.1 and C/EBPα synergistically program distinct response to NF-κB activation through establishing monocyte specific enhancers. Jin F, Li Y, Ren B, Natarajan R, Proc Natl Acad Sci 2011 108 5290 5295 10.1073/pnas.1017214108 21402921
70. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M, Cell 2008 132 958 970 10.1016/j.cell.2008. 01.018 18358809 (Pubitemid 351391952)
71. Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA. Sekiya T, Muthurajan UM, Luger K, Tulin AV, Zaret KS, Genes Dev 2009 23 804 809 10.1101/gad.1775509 19339686
72. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, Li W, Kaestner KH, Cell 2012 151 1608 1616 10.1016/j.cell.2012.11.018 23260146
73. Loss of FOXA1/2 is essential for the epithelial-to-mesenchymal transition in pancreatic cancer. Song Y, Washington MK, Crawford HC, Cancer Res 2010 70 2115 2125 10.1158/0008-5472.CAN-09-2979 20160041
74. Compensatory roles of Foxa1 and Foxa2 during lung morphogenesis. Wan H, Dingle S, Xu Y, Besnard V, Kaestner KH, Ang S-L, Wert S, Stahlman MT, Whitsett JA, J Biol Chem 2005 280 13809 13816 10.1074/jbc.M414122200 15668254 (Pubitemid 40517278)
75. Foxa2 regulates polarity and epithelialization in the endoderm germ layer of the mouse embryo. Burtscher I, Lickert H, Dev Camb Engl 2009 136 1029 1038
76. FOXA1 is an independent prognostic marker for ER-positive breast cancer. Mehta RJ, Jain RK, Leung S, Choo J, Nielsen T, Huntsman D, Nakshatri H, Badve S, Breast Cancer Res Treat 2012 131 881 890 10.1007/s10549-011-1482-6 21503684
77. Genome-wide mapping of in vivo protein-DNA interactions. Johnson DS, Mortazavi A, Myers RM, Wold B, Science 2007 316 1497 1502 10.1126/science. 1141319 17540862 (Pubitemid 46906620)
78. Bioconductor: open software development for computational biology and bioinformatics. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J, Genome Biol 2004 5 80 10.1186/gb-2004-5-10-r80 15461798
79. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Smyth GK, Stat Appl Genet Mol Biol 2004 3 rticle3 16646809
80. The UCSC genome browser and associated tools. Kuhn RM, Haussler D, Kent WJ, Brief Bioinform 2012 14 144 161 22908213
81. Fast and accurate long-read alignment with Burrows-Wheeler transform. Li H, Durbin R, Bioinformatics 2010 26 589 595 10.1093/bioinformatics/btp698 20080505
82. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Pickrell JK, Gaffney DJ, Gilad Y, Pritchard JK, Bioinformatics 2011 27 2144 2146 10.1093/bioinformatics/ btr354 21690102
83. Differential expression analysis for sequence count data. Anders S, Huber W, Genome Biol 2010 11 106 10.1186/gb-2010-11-10-r106 20979621
84. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W, Bioinformatics 2009 25 1952 1958 10.1093/bioinformatics/btp340 19505939
85. WGCNA: an R package for weighted gene co-expression network analysis. Langfelder P, Horvath S, BMC Bioinforma 2008 9 559 10.1186/1471-2105-9-559
86. ENCODE Data in the UCSC Genome Browser: year 5 update. Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ, Nucleic Acids Res 2012 doi: 10.1093/nar/gks1172
87. 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, Jensen LJ, von Mering C, Nucleic Acids Res 2011 39 suppl 1 561 D568 21045058
88. Network biology: understanding the cell's functional organization. Barabási A-L, Oltvai ZN, Nat Rev Genet 2004 5 101 113 10.1038/nrg1272 14735121 (Pubitemid 38160277)
89. Understanding network concepts in modules. Dong J, Horvath S, BMC Syst Biol 2007 1 24 10.1186/1752-0509-1-24 17547772 (Pubitemid 47079602)
90. Fast unfolding of communities in large networks. Blondel VD, Guillaume J-L, Lambiotte R, Lefebvre E, J Stat Mech Theory Exp 2008 2008 P10008
91. Laplacian dynamics and multiscale modular structure in networks. Lambiotte R, Delvenne J-C, Barahona M, arXiv 2008 08121770