Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74.
Article
Google Scholar
Consortium F, the RP, Clst, Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, et al. A promoter-level mammalian expression atlas. Nature. 2014;507(7493):462–70.
Article
Google Scholar
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014;507(7493):455–61.
Article
CAS
PubMed
PubMed Central
Google Scholar
Roadmap Epigenomics C, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317–30.
Article
Google Scholar
Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J. Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nat Methods. 2007;4(7):563–5.
Article
CAS
PubMed
Google Scholar
Haudry Y, Ramialison M, Paten B, Wittbrodt J, Ettwiller L. Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation. Nat Protoc. 2010;5(2):323–34.
Article
CAS
PubMed
Google Scholar
Corradin O, Scacheri PC. Enhancer variants: evaluating functions in common disease. Genome medicine. 2014;6(10):85.
Article
PubMed
PubMed Central
Google Scholar
Spitz F, Furlong EE. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012;13(9):613–26.
Article
CAS
PubMed
Google Scholar
Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007;316(5830):1497–502.
Article
CAS
PubMed
Google Scholar
van Steensel B, Delrow J, Henikoff S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet. 2001;27(3):304–8.
Article
CAS
PubMed
Google Scholar
Bouveret R, Waardenberg AJ, Schonrock N, Ramialison M, Doan T, de Jong D, Bondue A, Kaur G, Mohamed S, Fonoudi H, et al. NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets. elife. 2015;6:4. https://doi.org/10.7554/eLife.06942.
Google Scholar
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013;10(12):1213–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou X, Li D, Zhang B, Lowdon RF, Rockweiler NB, Sears RL, Madden PA, Smirnov I, Costello JF, Wang T. Epigenomic annotation of genetic variants using the roadmap epigenome browser. Nat Biotechnol. 2015;33(4):345–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Romanoski CE, Glass CK, Stunnenberg HG, Wilson L, Almouzni G. Epigenomics: roadmap for regulation. Nature. 2015;518(7539):314–6.
Article
CAS
PubMed
Google Scholar
Budden DM, Hurley DG, Crampin EJ. Predictive modelling of gene expression from transcriptional regulatory elements. Brief Bioinform. 2015;16(4):616–28.
Article
CAS
PubMed
Google Scholar
Suryamohan K, Halfon MS. Identifying transcriptional cis-regulatory modules in animal genomes. Wiley Interdiscip Rev Dev Biol. 2015;4(2):59–84.
Article
CAS
PubMed
Google Scholar
Kuttippurathu L, Hsing M, Liu Y, Schmidt B, Maskell DL, Lee K, He A, Pu WT, Kong SW. CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics. 2011;27(5):715–7.
Article
CAS
PubMed
Google Scholar
Machanick P, Bailey TL. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics. 2011;27(12):1696–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sharov AA, Ko MS. Exhaustive search for over-represented DNA sequence motifs with CisFinder. DNA Res. 2009;16(5):261–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res. 2012;40(4):e31.
Article
CAS
PubMed
Google Scholar
Zambelli F, Pesole G, Pavesi G. PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. Nucleic Acids Res. 2013;41(Web Server issue):W535–43. https://doi.org/10.1093/nar/gkt448. Epub 2013 Jun 7
Article
PubMed
PubMed Central
Google Scholar
Zhou J, Troyanskaya OG. Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods. 2015;12(10):931–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alipanahi B, Delong A, Weirauch MT, Frey BJ. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nat Biotech. 2015;33(8):831–8.
Article
CAS
Google Scholar
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Eberhard C, et al. The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016;44(W1):W3–W10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ambrosini G, Dreos R, Kumar S, Bucher P. The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data. BMC Genomics. 2016;17(1):938.
Article
PubMed
PubMed Central
Google Scholar
Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, Garcia Giron C, Hourlier T et al: The Ensembl gene annotation system. Database (Oxford). 2016;2016. doi: https://doi.org/10.1093/database/baw093. Print 2016.
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fleming JD, Pavesi G, Benatti P, Imbriano C, Mantovani R, Struhl K. NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors. Genome Res. 2013;23(8):1195–209.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vavouri T, Lehner B. Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Genome Biol. 2012;13(11):R110.
Article
PubMed
PubMed Central
Google Scholar
Kinsella RJ, Kahari A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford). 2011;2011:bar030.
Article
Google Scholar
Hume MA, Barrera LA, Gisselbrecht SS, Bulyk ML. UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res. 2015;43(Database issue):D117–22.
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, et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014;42(Database issue):D142–7.
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(Database issue):D195–202.
Article
CAS
PubMed
Google Scholar
Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, et al. HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res. 2016;44(D1):D116–25.
Article
CAS
PubMed
Google Scholar
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002;12(6):996–1006.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J. A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc. 2012;7(8):1551–68.
Article
CAS
PubMed
Google Scholar
Bailey TL. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics. 2011;27(12):1653–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. Transcriptional regulatory code of a eukaryotic genome. Nature. 2004;431(7004):99–104.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mahony S, Benos PV. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 2007;35(Web Server issue):W253–8. Epub 2007 May 3
Article
PubMed
PubMed Central
Google Scholar
Sulahian R, Chen J, Arany Z, Jadhav U, Peng S, Rustgi AK, Bass AJ, Srivastava A, Hornick JL, Shivdasani RA. SOX15 governs transcription in human stratified epithelia and a subset of esophageal adenocarcinomas. Cell Mol Gastroenterol Hepatol. 2015;1(6):598–609.e6.
Article
PubMed
PubMed Central
Google Scholar
Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K, et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 2005;3(1):e7.
Article
PubMed
Google Scholar
Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010;26(17):2204–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Linsley PS, Schelter J, Burchard J, Kibukawa M, Martin MM, Bartz SR, Johnson JM, Cummins JM, Raymond CK, Dai H, et al. Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression. Mol Cell Biol. 2007;27(6):2240–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Konig J, Zarnack K, Luscombe NM, Ule J. Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet. 2012;13(2):77–83.
Article
PubMed
Google Scholar
Ramialison M, Reinhardt R, Henrich T, Wittbrodt B, Kellner T, Lowy CM, Wittbrodt J. Cis-regulatory properties of medaka synexpression groups. Development. 2012;139(5):917–28.
Article
CAS
PubMed
Google Scholar
Houles T, Rodier G, Le Cam L, Sardet C, Kirsh O. Description of an optimized ChIP-seq analysis pipeline dedicated to genome wide identification of E4F1 binding sites in primary and transformed MEFs. Genom Data. 2015;5:368–70. https://doi.org/10.1016/j.gdata.2015.07.004. eCollection 2015 Sep
Article
PubMed
PubMed Central
Google Scholar
Huang W, Perez-Garcia P, Pokhilko A, Millar AJ, Antoshechkin I, Riechmann JL, Mas P. Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science. 2012;336(6077):75–9.
Article
CAS
PubMed
Google Scholar
Skalska L, Stojnic R, Li J, Fischer B, Cerda-Moya G, Sakai H, Tajbakhsh S, Russell S, Adryan B, Bray SJ. Chromatin signatures at notch-regulated enhancers reveal large-scale changes in H3K56ac upon activation. EMBO J. 2015;34(14):1889–904.
Article
CAS
PubMed
PubMed Central
Google Scholar
Winata CL, Kondrychyn I, Kumar V, Srinivasan KG, Orlov Y, Ravishankar A, Prabhakar S, Stanton LW, Korzh V, Mathavan S. Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish. PLoS Genet. 2013;9(10):e1003852.
Article
PubMed
PubMed Central
Google Scholar