Li MJ, Wang P, Liu X, Lim EL, Wang Z, Yeager M, Wong MP, Sham PC, Chanock SJ, Wang J: GWASdb: a database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 2012, 40: D1047-D1054. 10.1093/nar/gkr1182.
Article
CAS
PubMed
Google Scholar
Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM, Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS, Haussler D, Kent WJ: ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res. 2012, 40: D912-917. 10.1093/nar/gkr1012.
Article
CAS
PubMed
Google Scholar
Chen CY, Morris Q, Mitchell JA: Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. BMC Genomics. 2012, 13: 152-10.1186/1471-2164-13-152.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007, 39: 311-318. 10.1038/ng1966.
Article
CAS
PubMed
Google Scholar
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: Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010, 107: 21931-21936. 10.1073/pnas.1016071107.
Article
CAS
PubMed
PubMed Central
Google Scholar
Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, Saiakhova A, Bartels CF, Balasubramanian D, Myeroff L, Lutterbaugh J, Jarrar A, Kalady MF, Willis J, Moore JH, Tesar PJ, Laframboise T, Markowitz S, Lupien M, Scacheri PC: Epigenomic enhancer profiling defines a signature of colon cancer. Science. 2012, 336: 736-739. 10.1126/science.1217277.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wasserman NF, Aneas I, Nobrega MA: An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer. Genome Res. 2010, 20: 1191-1197. 10.1101/gr.105361.110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang X, Cowper-Sal lari R, Bailey SD, Moore JH, Lupien M: Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus. Genome Res. 2012, 22: 1437-1446. 10.1101/gr.135665.111.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gerasimova A, Chavez L, Li B, Seumois G, Greenbaum J, Rao A, Vijayanand P, Peters B: Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data. PLoS One. 2013, 8: e54359-10.1371/journal.pone.0054359.
Article
CAS
PubMed
PubMed Central
Google Scholar
Paul DS, Albers CA, Rendon A, Voss K, Stephens J, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH, Deloukas P: Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci. Genome Res. 2013, 23: 1130-1141. 10.1101/gr.155127.113.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M: Linking disease associations with regulatory information in the human genome. Genome Res. 2012, 22: 1748-1759. 10.1101/gr.136127.111.
Article
CAS
PubMed
PubMed Central
Google Scholar
Worsley-Hunt R, Bernard V, Wasserman WW: Identification of cis-regulatory sequence variations in individual genome sequences. Genome Med. 2011, 3: 65-10.1186/gm281.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andersen MC, Engstrom PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J: In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput Biol. 2008, 4: e5-10.1371/journal.pcbi.0040005.
Article
PubMed
PubMed Central
Google Scholar
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, et al: Architecture of the human regulatory network derived from ENCODE data. Nature. 2012, 489: 91-100. 10.1038/nature11245.
Article
CAS
PubMed
PubMed Central
Google Scholar
Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E: Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol. 2012, 13: R49-10.1186/gb-2012-13-9-r49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ward LD, Kellis M: HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 2012, 40: D930-D934. 10.1093/nar/gkr917.
Article
CAS
PubMed
Google Scholar
Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M: Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 2012, 22: 1790-1797. 10.1101/gr.137323.112.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rhie SK, Coetzee SG, Noushmehr H, Yan C, Kim JM, Haiman CA, Coetzee GA: Comprehensive functional annotation of seventy-one breast cancer risk Loci. PLoS One. 2013, 8: e63925-10.1371/journal.pone.0063925.
Article
PubMed
PubMed Central
Google Scholar
Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H: FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs. Nucleic Acids Res. 2012, 40: e139-10.1093/nar/gks542.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barenboim M, Manke T: ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation. Bioinformatics. 2013, 29: 2197-2198. 10.1093/bioinformatics/btt356.
Article
CAS
PubMed
PubMed Central
Google Scholar
Landi MT, Chatterjee N, Yu K, Goldin LR, Goldstein AM, Rotunno M, Mirabello L, Jacobs K, Wheeler W, Yeager M, Bergen AW, Li Q, Consonni D, Pesatori AC, Wacholder S, Thun M, Diver R, Oken M, Virtamo J, Albanes D, Wang Z, Burdette L, Doheny KF, Pugh EW, Laurie C, Brennan P, Hung R, Gaborieau V, McKay JD, Lathrop M, et al: A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. Am J Hum Genet. 2009, 85: 679-691. 10.1016/j.ajhg.2009.09.012.
Article
CAS
PubMed
PubMed Central
Google Scholar
R: A language and environment for statistical computing. [http://www.R-project.org]
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 JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5: R80-10.1186/gb-2004-5-10-r80.
Article
PubMed
PubMed Central
Google Scholar
A catalog of published genome-wide association studies. [http://www.genome.gov/gwastudies]
Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O’Donnell CJ, de Bakker PI: SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics. 2008, 24: 2938-2939. 10.1093/bioinformatics/btn564.
Article
CAS
PubMed
PubMed Central
Google Scholar
Teng L, Firpi HA, Tan K: Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers. Nucleic Acids Res. 2011, 39: 7371-7379. 10.1093/nar/gkr476.
Article
CAS
PubMed
PubMed Central
Google Scholar
Storey JD, Tibshirani R: Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003, 100: 9440-9445. 10.1073/pnas.1530509100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wasserman WW, Sandelin A: Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 2004, 5: 276-287. 10.1038/nrg1315.
Article
CAS
PubMed
Google Scholar
Lenhard B, Wasserman WW: TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics. 2002, 18: 1135-1136. 10.1093/bioinformatics/18.8.1135.
Article
CAS
PubMed
Google Scholar
Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A: JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 2010, 38: D105-D110. 10.1093/nar/gkp950.
Article
CAS
PubMed
Google Scholar
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B: Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012, 485: 376-380. 10.1038/nature11082.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ: The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 2006, 34: D590-598. 10.1093/nar/gkj144.
Article
CAS
PubMed
Google Scholar
Servant N, Lajoie BR, Nora EP, Giorgetti L, Chen CJ, Heard E, Dekker J, Barillot E: HiTC: exploration of high-throughput ‘C’ experiments. Bioinformatics. 2012, 28: 2843-2844. 10.1093/bioinformatics/bts521.
Article
CAS
PubMed
PubMed Central
Google Scholar
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: Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009, 459: 108-112. 10.1038/nature07829.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rowan S, Siggers T, Lachke SA, Yue Y, Bulyk ML, Maas RL: Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity. Genes Dev. 2010, 24: 980-985. 10.1101/gad.1890410.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edwards SL, Beesley J, French JD, Dunning AM: Beyond GWASs: illuminating the dark road from association to function. Am J Hum Genet. 2013, 93: 779-797. 10.1016/j.ajhg.2013.10.012.
Article
CAS
PubMed
PubMed Central
Google Scholar
Michailidou K, Hall P, Gonzalez-Neira A, Ghoussaini M, Dennis J, Milne RL, Schmidt MK, Chang-Claude J, Bojesen SE, Bolla MK, Wang Q, Dicks E, Lee A, Turnbull C, Rahman N, Fletcher O, Peto J, Gibson L, Dos Santos Silva I, Nevanlinna H, Muranen TA, Aittomaki K, Blomqvist C, Czene K, Irwanto A, Liu J, Waisfisz Q, Meijers-Heijboer H, Adank M, van der Luijt RB: Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Nat Genet. 2013, 45: 353-361. 10.1038/ng.2563. 361e351-352
Article
CAS
PubMed
PubMed Central
Google Scholar
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: ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009, 457: 854-858. 10.1038/nature07730.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jorgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, et al: An atlas of active enhancers across human cell types and tissues. Nature. 2014, 507: 455-461. 10.1038/nature12787.
Article
CAS
PubMed
Google Scholar
Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Bluthgen N, Dekker J, Heard E: Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012, 485: 381-385. 10.1038/nature11049.
Article
CAS
PubMed
PubMed Central
Google Scholar
Berlivet S, Paquette D, Dumouchel A, Langlais D, Dostie J, Kmita M: Clustering of tissue-specific Sub-TADs accompanies the regulation of HoxA genes in developing limbs. PLoS Genet. 2013, 9: e1004018-10.1371/journal.pgen.1004018.
Article
PubMed
PubMed Central
Google Scholar
Ghoussaini M, Fletcher O, Michailidou K, Turnbull C, Schmidt MK, Dicks E, Dennis J, Wang Q, Humphreys MK, Luccarini C, Baynes C, Conroy D, Maranian M, Ahmed S, Driver K, Johnson N, Orr N, Dos Santos Silva I, Waisfisz Q, Meijers-Heijboer H, Uitterlinden AG, Rivadeneira F, Hall P, Czene K, Irwanto A, Liu J, Nevanlinna H, Aittomaki K, Blomqvist C, Meindl A, et al: Genome-wide association analysis identifies three new breast cancer susceptibility loci. Nat Genet. 2012, 44: 312-318. 10.1038/ng.1049.
Article
CAS
PubMed
PubMed Central
Google Scholar
Park YY, Kim K, Kim SB, Hennessy BT, Kim SM, Park ES, Lim JY, Li J, Lu Y, Gonzalez-Angulo AM, Jeong W, Mills GB, Safe S, Lee JS: Reconstruction of nuclear receptor network reveals that NR2E3 is a novel upstream regulator of ESR1 in breast cancer. EMBO Mol Med. 2012, 4: 52-67. 10.1002/emmm.201100187.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang S, Chen L, Cui B, Chuang HY, Yu J, Wang-Rodriguez J, Tang L, Chen G, Basak GW, Kipps TJ: ROR1 is expressed in human breast cancer and associated with enhanced tumor-cell growth. PLoS One. 2012, 7: e31127-10.1371/journal.pone.0031127.
Article
CAS
PubMed
PubMed Central
Google Scholar
Uhrmacher S, Schmidt C, Erdfelder F, Poll-Wolbeck SJ, Gehrke I, Hallek M, Kreuzer KA: Use of the receptor tyrosine kinase-like orphan receptor 1 (ROR1) as a diagnostic tool in chronic lymphocytic leukemia (CLL). Leuk Res. 2011, 35: 1360-1366. 10.1016/j.leukres.2011.04.006.
Article
CAS
PubMed
Google Scholar
Zhi Q, Guo X, Guo L, Zhang R, Jiang J, Ji J, Zhang J, Zhang J, Chen X, Cai Q, Li J, Liu B, Zhu Z, Yu Y: Oncogenic miR-544 is an important molecular target in gastric cancer. Anticancer Agents Med Chem. 2013, 13: 270-275. 10.2174/1871520611313020013.
Article
CAS
PubMed
Google Scholar
Thayanithy V, Sarver AL, Kartha RV, Li L, Angstadt AY, Breen M, Steer CJ, Modiano JF, Subramanian S: Perturbation of 14q32 miRNAs-cMYC gene network in osteosarcoma. Bone. 2012, 50: 171-181. 10.1016/j.bone.2011.10.012.
Article
CAS
PubMed
Google Scholar
Luo Z, Zhang L, Li Z, Li X, Li G, Yu H, Jiang C, Dai Y, Guo X, Xiang J, Li G: An in silico analysis of dynamic changes in microRNA expression profiles in stepwise development of nasopharyngeal carcinoma. BMC Med Genomics. 2012, 5: 3-10.1186/1755-8794-5-3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nesbit CE, Tersak JM, Prochownik EV: MYC oncogenes and human neoplastic disease. Oncogene. 1999, 18: 3004-3016. 10.1038/sj.onc.1202746.
Article
CAS
PubMed
Google Scholar
Eisenman RN: Deconstructing myc. Genes Dev. 2001, 15: 2023-2030. 10.1101/gad928101.
Article
CAS
PubMed
Google Scholar
Li L, Davie JR: The role of Sp1 and Sp3 in normal and cancer cell biology. Ann Anat. 2010, 192: 275-283. 10.1016/j.aanat.2010.07.010.
Article
CAS
PubMed
Google Scholar
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW: JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014, 42: D142-147. 10.1093/nar/gkt997.
Article
CAS
PubMed
Google Scholar
Kulakovskiy IV, Medvedeva YA, Schaefer U, Kasianov AS, Vorontsov IE, Bajic VB, Makeev VJ: HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Res. 2013, 41: D195-D202. 10.1093/nar/gks1089.
Article
CAS
PubMed
Google Scholar
Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS: Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods. 2012, 9: 473-476. 10.1038/nmeth.1937.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ernst J, Kellis M: ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012, 9: 215-216. 10.1038/nmeth.1906.
Article
CAS
PubMed
PubMed Central
Google Scholar
Benos PV, Bulyk ML, Stormo GD: Additivity in protein-DNA interactions: how good an approximation is it?. Nucleic Acids Res. 2002, 30: 4442-4451. 10.1093/nar/gkf578.
Article
CAS
PubMed
PubMed Central
Google Scholar