Filters








129 Hits in 9.5 sec

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin
<span title="2009-11-10">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a  ...  As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions.  ...  ACKNOWLEDGEMENTS We thank Frank Grosveld and Eric Soler for permission to include into JASPAR of ChIP-seq derived profiles prior to publication.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp950">doi:10.1093/nar/gkp950</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19906716">pmid:19906716</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2808906/">pmcid:PMC2808906</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tt5yy255ufbxlj6v7xxsbiylwa">fatcat:tt5yy255ufbxlj6v7xxsbiylwa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190218105245/http://pdfs.semanticscholar.org/0c96/40952ace3d5466c36fd5255b82a6aea4fe0a.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0c/96/0c9640952ace3d5466c36fd5255b82a6aea4fe0a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp950"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808906" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

HGM 2010 Programme / Abstract

<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rn2dm7ildza6bbitx34suzwoay" style="color: black;">The HUGO Journal</a> </i> &nbsp;
We are currently RT-PCR-amplifying RNA from the lymphocytes of patients to identify aberrant transcripts.  ...  ACKNOWLEDGEMENTS HGM 2010 has received financial support from the following organisations. We would like to extend our utmost appreciation to them for all of their support.  ...  It builds on the JASPAR/PAZAR databases for transcription factor binding profiles with further information derived from miRBase and microRNA.org (for miRNA target predictions).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11568-010-9143-0">doi:10.1007/s11568-010-9143-0</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oykxd6u7snfi5o7m6tst7wi6yq">fatcat:oykxd6u7snfi5o7m6tst7wi6yq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200509010014/https://iris.unimore.it/retrieve/handle/11380/1114304/96179/HGM%25202010%2520-%2520Programs%26abstracts.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c9/2a/c92aaccb8b9781ee0dbfd1d66cfa4a97395e3787.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11568-010-9143-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Genomic repertoires of DNA-binding transcription factors across the tree of life

Varodom Charoensawan, Derek Wilson, Sarah A. Teichmann
<span title="2010-07-30">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Sequence-specific transcription factors (TFs) are important to genetic regulation in all organisms because they recognize and directly bind to regulatory regions on DNA.  ...  Only in eukaryotes does the same family of DNA-binding domain (DBD) occur multiple times within one polypeptide chain.  ...  ACKNOWLEDGEMENTS We thank Daniel Hebenstreit, Joseph Marsh, Anuphon Laohavisit, as well as anonymous referees for critical commentary on the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq617">doi:10.1093/nar/gkq617</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20675356">pmid:20675356</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2995046/">pmcid:PMC2995046</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jzgfue732fhe3n5ggxzxzpmy3u">fatcat:jzgfue732fhe3n5ggxzxzpmy3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302210225/http://pdfs.semanticscholar.org/a217/85d96b1e215a0c4fbef7e4e34598050df3ad.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a2/17/a21785d96b1e215a0c4fbef7e4e34598050df3ad.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq617"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995046" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An expansive human regulatory lexicon encoded in transcription factor footprints

Shane Neph, Jeff Vierstra, Andrew B. Stergachis, Alex P. Reynolds, Eric Haugen, Benjamin Vernot, Robert E. Thurman, Sam John, Richard Sandstrom, Audra K. Johnson, Matthew T. Maurano, Richard Humbert (+25 others)
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNaseI, leaving nucleotide-resolution footprints.  ...  We identify a stereotyped 50 base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters.  ...  Consequently, applying de novo motif discovery to the footprint compartments gleaned from multiple cell types should greatly expand our current knowledge of biologically active TF-binding motifs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature11212">doi:10.1038/nature11212</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22955618">pmid:22955618</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3736582/">pmcid:PMC3736582</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pjkrbgdw7nb3rdcpwddg4lvnte">fatcat:pjkrbgdw7nb3rdcpwddg4lvnte</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721101307/http://authors.fhcrc.org/613/1/NephNature_Sep2012.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/15/d9/15d9f29ba07639438f4d233d731f29f520ffafbc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature11212"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736582" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Global mapping of transcription factor motifs in human aging

David Alfego, Ulrich Rodeck, Andres Kriete, Klaus Roemer
<span title="2018-01-02">2018</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Acknowledgments The authors thank Nirupama Yalamanchili, Drexel University, Philadelphia, PA, and the Genomic Facility at the Wistar Institute, Philadelphia, PA, for support in experimental work leading  ...  JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 2010; 38(Database issue):D105-10.  ...  The molecular biology and nomenclature of the activating transcription factor/ cAMP responsive element binding family of transcription factors: activating transcription factor proteins and homeostasis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0190457">doi:10.1371/journal.pone.0190457</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29293662">pmid:29293662</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5749797/">pmcid:PMC5749797</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yp2qmaqj35fsfeevbwb2w5w4t4">fatcat:yp2qmaqj35fsfeevbwb2w5w4t4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302141733/http://pdfs.semanticscholar.org/a49a/91e1203d7133afcd8391a6486e353d36864f.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a4/9a/a49a91e1203d7133afcd8391a6486e353d36864f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0190457"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749797" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-wide analysis of androgen receptor binding and gene regulation in two CWR22-derived prostate cancer cell lines

Honglin Chen, Stephen J Libertini, Michael George, Satya Dandekar, Clifford G Tepper, Bushra Al-Bataina, Hsing-Jien Kung, Paramita M Ghosh, Maria Mudryj
<span title="">2010</span> <i title="Bioscientifica"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nsr5e5h76rfcxoqye3esecdftq" style="color: black;">Endocrine-Related Cancer</a> </i> &nbsp;
The most prominent function of transcripts that were direct AR targets was transcriptional regulation, although only one transcriptional regulator, CCAAT/enhancer binding protein δ, was commonly regulated  ...  Our results indicate that the AR regulates the expression of different transcripts in the two lines, and demonstrate the versatility of the AR-regulated gene expression program in prostate tumors.  ...  Acknowledgements We thank Dr Elizabeth Wilson for the CWR-R1 cells and greatly appreciate the expert technical assistance and consultation of Ryan R Davis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1677/erc-10-0081">doi:10.1677/erc-10-0081</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20634343">pmid:20634343</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3539310/">pmcid:PMC3539310</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ztb5la3rpnexrjvsyyx4lcibbq">fatcat:ztb5la3rpnexrjvsyyx4lcibbq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219071318/http://pdfs.semanticscholar.org/1a72/f3eb6dbd713dbf400ff69a72092190ba541a.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1a/72/1a72f3eb6dbd713dbf400ff69a72092190ba541a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1677/erc-10-0081"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539310" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cooperativity of Stress-Responsive Transcription Factors in Core Hypoxia-Inducible Factor Binding Regions

Diego Villar, Amaya Ortiz-Barahona, Laura Gómez-Maldonado, Nuria Pescador, Fátima Sánchez-Cabo, Hubert Hackl, Benjamin A. T. Rodriguez, Zlatko Trajanoski, Ana Dopazo, Tim H. M. Huang, Pearlly S. Yan, Luis del Peso (+1 others)
<span title="2012-09-24">2012</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
We obtained a core set of bona fide HIF binding regions by integrating multiple HIF1 DNA binding and hypoxia expression profiling datasets.  ...  The transcriptional response driven by Hypoxia-inducible factor (HIF) is central to the adaptation to oxygen restriction.  ...  Acknowledgments We thank Gernot Stocker (Innsbruck Medical University, Austria) for expert assistance on the implementation of Perl programs for transcription factor binding site predictions and other  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0045708">doi:10.1371/journal.pone.0045708</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23029193">pmid:23029193</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3454324/">pmcid:PMC3454324</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bgvsydompfd23gyaraumq3bryu">fatcat:bgvsydompfd23gyaraumq3bryu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20140208012951/http://digital.csic.es:80/bitstream/10261/57366/1/Plos%20One%20%20%202012%20vol7%20n9%20ppe45708.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/63/a9/63a99b382068222575181fc915873bf343cc607a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0045708"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3454324" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genomic Features of the Human Dopamine Transporter Gene and Its Potential Epigenetic States: Implications for Phenotypic Diversity

Elena Shumay, Joanna S. Fowler, Nora D. Volkow, Axel Imhof
<span title="2010-06-10">2010</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Hence, our understanding of the control of the DAT protein product is incomplete; having this knowledge is critical, since DAT plays the major role in the brain's dopaminergic circuitry.  ...  However, the abundance of research data has not clarified the biological mechanism of DAT regulation; similarly, studies of DAT genotype-phenotype associations yielded inconsistent results.  ...  Ruben Baler for helpful discussions and suggestions on the organization of the manuscript, Dr. Fritz Henn for long-standing support, and Dr. Avril Woodhead for editing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0011067">doi:10.1371/journal.pone.0011067</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20548783">pmid:20548783</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2883569/">pmcid:PMC2883569</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ne7rn76wtnedfjvjvld73dda5i">fatcat:ne7rn76wtnedfjvjvld73dda5i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170925180153/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0011067&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/58/c6/58c6c040c12d0b8ebab21d539298beeca6c8595d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0011067"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2883569" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome wide predictions of miRNA regulation by transcription factors

Matthew Ruffalo, Ziv Bar-Joseph
<span title="2016-09-01">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
While much work has focused on trying to experimentally and computationally determine the set of transcription-factors (TFs) and microRNAs (miRNAs) that regulate genes in these networks, relatively little  ...  work has focused on inferring the regulation of miRNAs by TFs.  ...  This project is funded, in part, under a grant (#4100070287) with the Pennsylvania Department of Health.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btw452">doi:10.1093/bioinformatics/btw452</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27587697">pmid:27587697</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b6smuuaevvbijfdsw7zwqjacaq">fatcat:b6smuuaevvbijfdsw7zwqjacaq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728223418/https://watermark.silverchair.com/btw452.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAcEwggG9BgkqhkiG9w0BBwagggGuMIIBqgIBADCCAaMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMbEvvicXtUVMMIdyzAgEQgIIBdBNXstjNgLOmOq2DsPvXp8vFvAy9BxcsL1WjZTWPJVTR7hjZt5OpRwVEUnIAiH4pfGXckxDB7OQgKQmQ3OvSIzkvjeUk-bsi5IJ6iu4-2DfkmZMZwz6PrgggM1WKAEN7HPLNgYRTZ5T6xb2puX7h83zwWw7n0DMCQ3B2yMW-PiAFG_GHHUOh_HYwbSwRRbGt_cs9n-HiQFqLntygoHCP0kFSzPiJUhhOHSW6g1XMaAspwfYZtN-pEuyZpZ-MS7JdIIRrv-VzutXTuSlx9BjZaDIkM02ickR8ImIvx49RKDtHR1he1sHZL1iK4RFkrB67WShz8fTepn006yRVy-N1jqL7xy4h3yBVjmENsB6X2-xhsVEXLd_TSMszfonQdYqpIanZ684VGF_5MkTAIRerQOwHwdZYIneY7RTTt-UlsC5iHDEwPWCCMwi5l38LA6nbbDSdth2rzJy9Wr_pRF0PhvBj9OTcafqyFWDkZjeriJEZVjVYMQ" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/32/90/329084988f07f9f51ecdbb3da074d3c525367ba7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btw452"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Key regulators control distinct transcriptional programmes in blood progenitor and mast cells

F. J. Calero-Nieto, F. S. Ng, N. K. Wilson, R. Hannah, V. Moignard, A. I. Leal-Cervantes, I. Jimenez-Madrid, E. Diamanti, L. Wernisch, B. Gottgens
<span title="2014-04-23">2014</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xcjlfiweh5bfpiome6ieuwel2a" style="color: black;">EMBO Journal</a> </i> &nbsp;
Despite major advances in the generation of genome-wide binding maps, the mechanisms by which transcription factors (TFs) regulate cell type identity have remained largely obscure.  ...  Finally, we show that the known mast cell regulators Mitf and c-fos likely contribute to the global reorganisation of TF binding profiles.  ...  Acknowledgments Work in the authors' laboratories is supported by grants from Leukaemia and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/embj.201386825">doi:10.1002/embj.201386825</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24760698">pmid:24760698</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4168288/">pmcid:PMC4168288</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rogqni2ntrfxxazhpjxkjn34xa">fatcat:rogqni2ntrfxxazhpjxkjn34xa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430090436/http://emboj.embopress.org/content/embojnl/33/11/1212.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1a/e0/1ae056b4193715c1bf372c250a983951cc54110f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/embj.201386825"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168288" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Identification and Computational Analysis of Gene Regulatory Elements

Leila Taher, Leelavati Narlikar, Ivan Ovcharenko
<span title="">2015</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kkiieryxvje2diqdkb2ax2yiem" style="color: black;">Cold Spring Harbor Protocols</a> </i> &nbsp;
Over the last two decades, advances in experimental and computational technologies have greatly facilitated genomic research.  ...  Here we describe some of these approaches and provide an account of our current understanding of the complex landscape of the human genome.  ...  ACKNOWLEDGMENTS This research was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine and by an Early Career Fellowship to L.N. from the Wellcome  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/pdb.top083642">doi:10.1101/pdb.top083642</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25561628">pmid:25561628</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5885252/">pmcid:PMC5885252</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qdzm42aypzdz5askrohbwnswny">fatcat:qdzm42aypzdz5askrohbwnswny</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228033711/http://pdfs.semanticscholar.org/8b8d/793c3be20be89af0213a820db7c693b19055.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8b/8d/8b8d793c3be20be89af0213a820db7c693b19055.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/pdb.top083642"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885252" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

Cyrille Lepoivre, Aurélie Bergon, Fabrice Lopez, Narayanan B Perumal, Catherine Nguyen, Jean Imbert, Denis Puthier
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions.  ...  The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-13-19">doi:10.1186/1471-2105-13-19</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22292669">pmid:22292669</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3395838/">pmcid:PMC3395838</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nzml5gu2gnh2bnuteomu77u5au">fatcat:nzml5gu2gnh2bnuteomu77u5au</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190323022446/https://core.ac.uk/download/pdf/52448141.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/88/70883b5ccbabbe593e6c55300493a660afe99c85.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-13-19"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3395838" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

Naoki Osato
<span title="">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
To address these issues, I predicted human 14 transcriptional target genes using open chromatin regions, ChIP-seq data and DNA 15 binding sequences of transcription factors in databases, and examined functional  ...  These analyses and 41 characters of human putative transcriptional target genes would be useful to examine 42 the criteria of enhancer-promoter assignments and to predict the novel mechanisms and 43 factors  ...  Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, 710 Yusuf D, Lenhard B, Wasserman WW, Sandelin A: JASPAR 2010: the greatly 711 expanded open-access database of transcription factor  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-017-4339-5">doi:10.1186/s12864-017-4339-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29363429">pmid:29363429</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5780744/">pmcid:PMC5780744</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pbtqjkr6gzeb7jwhefwfwbhdka">fatcat:pbtqjkr6gzeb7jwhefwfwbhdka</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724193817/https://www.biorxiv.org/content/biorxiv/early/2017/07/16/085654.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0d/bf/0dbf14f575a474fc76dddb55808918973b8b9ffd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-017-4339-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780744" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Stage-Specific OTX2 Regulatory Network and Maturation-Associated Gene Programs Are Inherent Barriers to RPE Neural Competency

Jared A. Tangeman, J. Raúl Pérez-Estrada, Emily Van Zeeland, Lin Liu, Alexandra Danciutiu, Erika Grajales-Esquivel, Byran Smucker, Chun Liang, Katia Del Rio-Tsonis
<span title="2022-04-19">2022</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4dl6zyzmsrhczjurbzfc3hrzn4" style="color: black;">Frontiers in Cell and Developmental Biology</a> </i> &nbsp;
Predicted OTX2 binding motifs undergo robust accessibility increases in E5 RPE, many of which coincide with putative regulatory elements for genes known to facilitate RPE differentiation and maturation  ...  The retinal pigment epithelium (RPE) exhibits a diverse range of plasticity across vertebrates and is a potential source of cells for the regeneration of retinal neurons.  ...  The authors extend their appreciation to Anthony Sallese (Miami University) for critical reading of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fcell.2022.875155">doi:10.3389/fcell.2022.875155</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35517508">pmid:35517508</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC9062105/">pmcid:PMC9062105</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k5lm4w4gwfbj3a4atr5rmjsbwi">fatcat:k5lm4w4gwfbj3a4atr5rmjsbwi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220426033705/https://fjfsdata01prod.blob.core.windows.net/articles/files/875155/pubmed-zip/.versions/2/.package-entries/fcell-10-875155-r1/fcell-10-875155.pdf?sv=2018-03-28&amp;sr=b&amp;sig=ztur2QQdNmovjL1sgHbP7p0zjYf9cE1ubZsCjGUY%2FBY%3D&amp;se=2022-04-26T03%3A37%3A34Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fcell-10-875155.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/34/b4/34b43800d9702603a4e37a0ccd359d9f9607539a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fcell.2022.875155"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9062105" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

Abdenour Soufi, Greg Donahue, Kenneth S. Zaret
<span title="">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iwommhyo5bdk7c3u37mhjzexfe" style="color: black;">Cell</a> </i> &nbsp;
The ectopic expression of transcription factors can reprogram cell fate, yet it is unknown how the initial binding of factors to the genome relates functionally to the binding seen in the minority of cells  ...  We find diverse aspects of initial factor binding that must be overcome in the minority of cells that become reprogrammed.  ...  Kim for comments on the manuscript; and K. Kaestner and J. Schug for sequencing by the UPenn Diabetes Research Center Functional Genomics Gore (P30-DK19525).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cell.2012.09.045">doi:10.1016/j.cell.2012.09.045</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23159369">pmid:23159369</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3508134/">pmcid:PMC3508134</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/25mm2pyh6vhozcx3sys3a22f4i">fatcat:25mm2pyh6vhozcx3sys3a22f4i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170929172307/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/7eb/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDA5Mjg2NzQxMjAxMjk4Ng%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5a/d2/5ad2e2c1f50d033aa430e307342d76ba5ad1172c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cell.2012.09.045"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3508134" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 129 results