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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Comparative annotation of functional regions in the human genome using epigenomic data.
TL;DR: A machine-learning method called ChroModule is developed to annotate the epigenetic states in eight ENCyclopedia Of DNA Elements cell types and it is found that invariable and variable epigeneticStates across cell types correspond to housekeeping functions and stimulus response, respectively.
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Somitogenesis in the Anole Lizard and Alligator Reveals Evolutionary Convergence and Divergence in the Amniote Segmentation Clock
Walter L. Eckalbar,Eris Lasku,Carlos Infante,Ruth M. Elsey,Glenn J. Markov,April N. Allen,Jason J. Corneveaux,Jonathan B. Losos,Dale F. DeNardo,Matthew J. Huentelman,Jeanne Wilson-Rawls,Alan Rawls,Kenro Kusumi +12 more
TL;DR: Comparisons among vertebrate model systems and in situ hybridization analysis of somite-stage embryos yield novel insights into features of the segmentation clock that are evolutionarily basal to amniotes versus those that are specific to mammals, Lepidosaurian reptiles, or Archosaurusian reptiles.
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Transcriptional regulatory networks underlying gene expression changes in Huntington's disease
Seth A. Ament,Seth A. Ament,Jocelynn R. Pearl,Jocelynn R. Pearl,Jeffrey P. Cantle,Robert M. Bragg,Peter J Skene,Sydney R. Coffey,Dani E Bergey,Vanessa C. Wheeler,Marcy E. MacDonald,Nitin S. Baliga,Jim Rosinski,Leroy Hood,Jeffrey B. Carroll,Nathan D. Price +15 more
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SNPs occur in regions with less genomic sequence conservation.
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Identification of molecular compartments and genetic circuitry in the developing mammalian kidney
Jing Yu,M. Todd Valerius,Mary Duah,Karl Staser,Jennifer K. Hansard,Jinjin Guo,Jill A. McMahon,Joe E. Vaughan,Diane Faria,Kylie Georgas,Bree Rumballe,Qun Ren,A. Michaela Krautzberger,Jan Philipp Junker,Rathi D Thiagarajan,Philip Machanick,Paul A. Gray,Alexander van Oudenaarden,David H. Rowitch,Charles D. Stiles,Qiufu Ma,Sean M. Grimmond,Timothy L. Bailey,Melissa H. Little,Andrew P. McMahon +24 more
TL;DR: A comprehensive genome-scale in situ expression screen of 921 transcriptional regulators in the developing mammalian urogenital system identified novel markers and cell types associated with development and patterning of the urinary system and predicted transcriptional control mechanisms that regulate cell differentiation.
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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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