TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes
V. Matys,Olga V. Kel-Margoulis,Ellen Fricke,Ines Liebich,Sigrid Land,A. Barre-Dirrie,Ingmar Reuter,D. Chekmenev,Mathias Krull,Klaus Hornischer,Nico Voss,Philip Stegmaier,Birgit Lewicki-Potapov,H. Saxel,Alexander E. Kel,Edgar Wingender +15 more
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TLDR
The TRANSFAC® database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel® on composite elements have been further enhanced on various levels.Abstract:
The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match and Patch provides increased functionality for TRANSFAC. The list of databases which are linked to the common GENE table of TRANSFAC and TRANSCompel has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD and TRANSPRO. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC, in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.read more
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Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling
Stephen C. Mack,Kristian W. Pajtler,Kristian W. Pajtler,Lukas Chavez,Lukas Chavez,Konstantin Okonechnikov,Kelsey C. Bertrand,Kelsey C. Bertrand,Xiuxing Wang,Xiuxing Wang,Xiuxing Wang,Serap Erkek,Alexander J. Federation,Anne Song,Anne Song,Christine Lee,Christine Lee,Xin Wang,Laura McDonald,James J. Morrow,Alina Saiakhova,Patrick Sin-Chan,Qiulian Wu,Qiulian Wu,Qiulian Wu,Kulandaimanuvel Antony Michaelraj,Tyler E. Miller,Tyler E. Miller,Christopher G. Hubert,Christopher G. Hubert,Marina Ryzhova,Livia Garzia,Laura K. Donovan,Stephen M. Dombrowski,Stephen M. Dombrowski,Daniel C. Factor,Betty Luu,Claudia L.L. Valentim,Claudia L.L. Valentim,Ryan C. Gimple,Ryan C. Gimple,Ryan C. Gimple,Andrew R. Morton,Andrew R. Morton,Leo J.Y. Kim,Leo J.Y. Kim,Leo J.Y. Kim,Briana C. Prager,Briana C. Prager,Briana C. Prager,John J.Y. Lee,Xiaochong Wu,Jennifer Zuccaro,Yuan Yao Thompson,Borja L. Holgado,Jüri Reimand,Jüri Reimand,Susan Q. Ke,Susan Q. Ke,Adam Tropper,Adam Tropper,Sisi Lai,Sisi Lai,Senthuran Vijayarajah,Senthuran Vijayarajah,Sylvia Doan,Vaidehi Mahadev,Vaidehi Mahadev,Ana Fernandez Miñan,Susanne Gröbner,Matthias Lienhard,Marc Zapatka,Zhiqin Huang,Kenneth Aldape,Angel M. Carcaboso,Peter J. Houghton,Stephen T. Keir,Till Milde,Till Milde,Hendrik Witt,Hendrik Witt,Yan Li,Chao Jun Li,Xiu-Wu Bian,David T.W. Jones,Ian C. Scott,Sheila K. Singh,Annie Huang,Annie Huang,Peter B. Dirks,Eric Bouffet,Eric Bouffet,James E. Bradner,Vijay Ramaswamy,Nada Jabado,James T. Rutka,Paul A. Northcott,Mathieu Lupien,Peter Lichter,Andrey Korshunov,Andrey Korshunov,Peter C. Scacheri,Stefan M. Pfister,Stefan M. Pfister,Marcel Kool,Michael D. Taylor,Jeremy N. Rich,Jeremy N. Rich,Jeremy N. Rich +108 more
TL;DR: Through profiling of transcriptional enhancers, this study provides a framework for target and drug discovery in other cancers that lack known genetic drivers and are therefore difficult to treat, and reveals putative oncogenes, molecular targets and pathways.
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Yat T. Tang,Xin Gao,Bruce A. Rosa,Sahar Abubucker,Kymberlie Hallsworth-Pepin,John Martin,Rahul Tyagi,Esley M. Heizer,Xu Zhang,Veena Bhonagiri-Palsikar,Patrick Minx,Wesley C. Warren,Qi Wang,Bin Zhan,Peter J. Hotez,Paul W. Sternberg,Paul W. Sternberg,Annette M. Dougall,Soraya Gaze,Jason Mulvenna,Javier Sotillo,Shoba Ranganathan,Shoba Ranganathan,Élida Mara Leite Rabelo,Richard K. Wilson,Philip L. Felgner,Jeffrey M. Bethony,John M. Hawdon,Robin B. Gasser,Alex Loukas,Makedonka Mitreva +30 more
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Comparative analysis of regulatory information and circuits across distant species
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TL;DR: In this article, the genome-wide binding locations of 165 human, 93 worm and 52 fly transcription regulatory factors were mapped for a total of 1,019 data sets from diverse cell types, developmental stages, or conditions in the three species, of which 498 (48.9%) are presented here for the first time.
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BioPAX A Community Standard for Pathway Data Sharing | NIST
TL;DR: Thousands of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available, and large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.
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The CRTC1-SIK1 pathway regulates entrainment of the circadian clock.
Aarti Jagannath,R Butler,R Butler,Godinho Sih.,Godinho Sih.,Yvonne Couch,Laurence A. Brown,Sridhar R. Vasudevan,Kevin C. Flanagan,Daniel C. Anthony,Grant C. Churchill,Wood Mja.,G Steiner,Martin Ebeling,M Hossbach,Joseph G. Wettstein,Giles E. Duffield,Silvia Gatti,Mark W. Hankins,Russell G. Foster,Stuart N. Peirson +20 more
TL;DR: Analysis of the light-regulated transcriptome of the SCN has identified a key role for salt inducible kinase 1 (SIK1) and CREB-regulated transcription coactivator 1 (CRTC1) in clock re-setting and provides a potential target for the regulation of circadian rhythms.
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