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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Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines.
Luciane T. Kagohara,Fernando T. Zamuner,Emily F. Davis-Marcisak,Gaurav Sharma,Michael Considine,Jawara Allen,Srinivasan Yegnasubramanian,Daria A. Gaykalova,Elana J. Fertig +8 more
TL;DR: It is shown that immediate adaptive transcriptional and epigenetic changes induced by cetuximab are heterogeneous and cell type dependent; and independent mechanisms of resistance arise while tumour cells are still sensitive to therapy.
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Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes
Nicholas P. Semenkovich,Joseph D. Planer,Philip P. Ahern,Nicholas W. Griffin,Charles Y. Lin,Jeffrey I. Gordon +5 more
TL;DR: The results support the notion that epigenetic modifications help define microbial community-affiliated functional features of host immune cell lineages.
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A chromatin-independent role of polycomb-like 1 to stabilize p53 and promote cellular quiescence
Gerard L. Brien,Evan Healy,Emilia Jerman,Eric Conway,Elisa Fadda,Darragh O'Donovan,Andrei V. Krivtsov,Alan M. Rice,Conor J. Kearney,Andrew Flaus,Simon S. McDade,Seamus J. Martin,Aoife McLysaght,David J. O'Connell,Scott A. Armstrong,Adrian P. Bracken +15 more
TL;DR: The functional bifurcation of PCL proteins is illustrated, which act in both a chromatin-dependent and a Chromatin-independent manner to regulate the INK4A and p53 pathways.
Journal ArticleDOI
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines
TL;DR: Mammalian HOT regions are regulatory hubs that integrate the signals from diverse regulatory pathways to quantitatively tune the promoter for RNA polymerase II recruitment.
Journal ArticleDOI
Systematic Dissection of Coding Exons at Single Nucleotide Resolution Supports an Additional Role in Cell-Specific Transcriptional Regulation
Ramon Y. Birnbaum,Rupali P Patwardhan,Mee J. Kim,Gregory M. Findlay,Beth Martin,Jingjing Zhao,Robert J.A. Bell,Robin P. Smith,Angel A. Ku,Jay Shendure,Nadav Ahituv +10 more
TL;DR: The results demonstrate that eExon mutations could lead to multiple phenotypes by disrupting both the protein sequence and enhancer activity and that enhancers can have distinct mutation profiles in different cell types.
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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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