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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Relevance of iPSC-derived human PGC-like cells at the surface of embryoid bodies to prechemotaxis migrating PGCs.
Shino Mitsunaga,Junko Odajima,Shiomi Yawata,Keiko Shioda,Chie Owa,Kurt J. Isselbacher,Jacob H. Hanna,Toshi Shioda +7 more
TL;DR: This study shows that transcriptionally consistent hPGCLCs can be readily produced from hiPSCs after transition of their pluripotency from the primed state using various methods and that h PGCLCs resemble the early-stage PGCs randomly migrating in the midline region of human embryos before initiation of the CXCL12/SDF1-guided chemotaxis.
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A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of Myogenesis
Brian W. Busser,Leila Taher,Yongsok Kim,Terese Tansey,Molly J. Bloom,Ivan Ovcharenko,Alan M. Michelson +6 more
TL;DR: In this paper, a DNA-based enhancer sequence classifier was used to identify the TF binding sites (TFBSs) governing the transcription of a co-expressed gene set.
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Identification and Characterization of Functional Risk Variants for Colorectal Cancer Mapping to Chromosome 11q23.1
Michela Biancolella,Barbara K. Fortini,Stephanie Tring,Sarah J. Plummer,Gustavo Mendoza-Fandiño,Jaana Hartiala,Michael J. Hitchler,Chunli Yan,Fredrick R. Schumacher,David V. Conti,Christopher K. Edlund,Houtan Noushmehr,Houtan Noushmehr,Simon G. Coetzee,Simon G. Coetzee,Robert S. Bresalier,Dennis J. Ahnen,Elizabeth L. Barry,Benjamin P. Berman,Judd C. Rice,Gerhard A. Coetzee,Graham Casey +21 more
TL;DR: It is reasoned that rs3802842 is not the functional single-nucleotide polymorphism (SNP), but is in linkage disequilibrium (LD) with a functional SNP(s), and that C11orf53, C11orc92 and C 11orf93 represent novel candidate target genes involved in CRC etiology.
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Steroid Hormone Modulation of RET Through Two Estrogen Responsive Enhancers in Breast Cancer
TL;DR: It is demonstrated that endogenous RET expression and RET -49.8 regulatory activity are cooperatively regulated by E2 and RA in breast cancer cells, and ESR1 is sufficient to mediate the E2-induced enhancer activity of RET - 49.8.
Journal ArticleDOI
Cross Talk Between GH-Regulated Transcription Factors HNF6 and CUX2 in Adult Mouse Liver.
TL;DR: HNF6 binding was sex independent at a majority of its binding sites, and HNF6 peaks were frequently associated with cobinding by multiple other liver transcription factors, consistent with HNF 6 playing a global regulatory role in both male and female liver.
References
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TRANSFAC®: transcriptional regulation, from patterns to profiles
V. Matys,Ellen Fricke,Robert Geffers,Ellen Gößling,Martin Haubrock,Reinhard Hehl,Klaus Hornischer,Dagmar Karas,Alexander E. Kel,Olga V. Kel-Margoulis,Dorothee-U. Kloos,Sigrid Land,Birgit Lewicki-Potapov,Holger Michael,Richard Münch,Ingmar Reuter,Stella Rotert,H. Saxel,Maurice Scheer,S. Thiele,Edgar Wingender +20 more
TL;DR: The TRANSFAC database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data.
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