i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly
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Stein Aerts | Gert Hulselmans | Delphine Potier | Hana Imrichová | Zeynep Kalender Atak | S. Aerts | Gert Hulselmans | Hana Imrichová | Z. Atak | Delphine Potier | Gert J. Hulselmans
[1] A. Visel,et al. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. , 2010, Genome research.
[2] Martin C. Frith,et al. Cluster-Buster: finding dense clusters of motifs in DNA sequences , 2003, Nucleic Acids Res..
[3] Valer Gotea,et al. DiRE: identifying distant regulatory elements of co-expressed genes , 2008, Nucleic Acids Res..
[4] Philipp Bucher,et al. UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks , 2012, Nucleic Acids Res..
[5] Michael Q. Zhang,et al. Integrative analysis of 111 reference human epigenomes , 2015, Nature.
[6] Shawn M. Gillespie,et al. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. , 2014, Cancer cell.
[7] J. van Helden,et al. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets , 2011, Nucleic acids research.
[8] William Stafford Noble,et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors , 2012, Genome research.
[9] Bin Chen,et al. Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool , 2013, Bioinform..
[10] David J. Arenillas,et al. oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets , 2012, G3: Genes | Genomes | Genetics.
[11] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[12] Obi L. Griffith,et al. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation , 2006, Bioinform..
[13] Aaron R. Quinlan,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .
[14] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[15] Jason B. Ernst,et al. Integrating multiple evidence sources to predict transcription factor binding in the human genome. , 2010, Genome research.
[16] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[17] Trey Ideker,et al. Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..
[18] Mathieu Blanchette,et al. PReMod: a database of genome-wide mammalian cis-regulatory module predictions , 2006, Nucleic Acids Res..
[19] Cory Y. McLean,et al. GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.
[20] Martin Kuiper,et al. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..
[21] Mary Goldman,et al. The UCSC Genome Browser database: extensions and updates 2013 , 2012, Nucleic Acids Res..
[22] S. Aerts,et al. i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules , 2012, Nucleic acids research.
[23] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[24] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[25] Philip Cayting,et al. An encyclopedia of mouse DNA elements (Mouse ENCODE) , 2012, Genome Biology.
[26] C. Glass,et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.
[27] Brad T. Sherman,et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.
[28] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[29] Israel Steinfeld,et al. BMC Bioinformatics BioMed Central , 2008 .
[30] Mary Goldman,et al. The UCSC Genome Browser database: extensions and updates 2011 , 2011, Nucleic Acids Res..
[31] Terrence S. Furey,et al. The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..
[32] Joshua M. Stuart,et al. A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.
[33] Helga Thorvaldsdóttir,et al. Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..
[34] Panayiotis V. Benos,et al. DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies , 2007, PLoS Comput. Biol..
[35] Thomas Whitington,et al. Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites , 2013, Cell.
[36] Alan M. Moses,et al. In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.
[37] P. Åman,et al. Fusion genes in solid tumors. , 1999, Seminars in cancer biology.
[38] ENCODEConsortium,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[39] Stein Aerts,et al. iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections , 2014, PLoS Comput. Biol..
[40] Bassem A. Hassan,et al. Gene prioritization through genomic data fusion , 2006, Nature Biotechnology.
[41] Philip Machanick,et al. MEME-ChIP: motif analysis of large DNA datasets , 2011, Bioinform..
[42] David J. Arenillas,et al. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles , 2009, Nucleic Acids Res..
[43] Clifford A. Meyer,et al. Cistrome: an integrative platform for transcriptional regulation studies , 2011, Genome Biology.
[44] S. Aerts,et al. Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state , 2015, Nature Communications.