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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Myeloid malignancies with chromosome 5q deletions acquire a dependency on an intrachromosomal NF-κB gene network.
Jing Fang,Brenden Barker,Lyndsey Bolanos,Xiaona Liu,Andres Jerez,Hideki Makishima,Susanne Christie,Xiaoting Chen,Xiaoting Chen,Dinesh S. Rao,H. Leighton Grimes,Kakajan Komurov,Matthew T. Weirauch,Jose A. Cancelas,Jose A. Cancelas,Jaroslaw P. Maciejewski,Daniel T. Starczynowski,Daniel T. Starczynowski +17 more
TL;DR: Del(5q) HR MDS/AML employs an intrachromosomal gene network involving loss of miR-146a and haploid overexpression of p62 via NF-κB to sustain TRAF6/NF-κBs signaling for cell survival and proliferation.
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Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling
Astrid L. Basse,Karen Dixen,Rachita Yadav,M. P. Tygesen,Klaus Qvortrup,Karsten Kristiansen,Bjørn Quistorff,Ramneek Gupta,Jun Wang,Jacob B. Hansen +9 more
TL;DR: Using global gene expression profiling of the postnatal BAT to WAT transformation in sheep, novel insight is provided into adipose tissue plasticity in a large mammal, including identification of novel transcriptional components linked to adipOSE tissue remodeling.
Journal ArticleDOI
Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes
Ryoko Harada,Charles Vadnais,Laurent Sansregret,Lam Leduy,Ginette Bérubé,François Robert,Alain Nepveu +6 more
TL;DR: Constutive expression of p110 CUX1 led to a premature and more robust induction of replication genes during cell cycle progression, and stimulated the long-term replication of a plasmid bearing the oriP replicator of Epstein Barr virus (EBV).
Journal ArticleDOI
Histone Methylation Marks Play Important Roles in Predicting the Methylation Status of CpG Islands
TL;DR: The results imply the important roles of histone methylation marks in affecting the methylation status of CpG islands, and suggest the established open environment may be a prerequisite for or a consequence of the function implementation of zinc finger proteins that could protect C pG islands from DNA methylation.
Journal ArticleDOI
Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations
Alexander E. Kel,T. Konovalova,T. Waleev,E. Cheremushkin,Olga V. Kel-Margoulis,Edgar Wingender +5 more
TL;DR: Here a new approach for defining promoter models based on the composition of TF binding sites and their pairs is presented, utilizing a multicomponent fitness function for selection of the promoter model that fits best to the observed gene expression profile.
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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