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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EDGEdb: a transcription factor-DNA Interaction database for the analysis of C. elegans differential gene expression
TL;DR: EDGEdb provides a protein-DNA -and protein-protein interaction resource for C. elegans transcription factors and a framework for similar databases for other organisms.
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The genome of the Antarctic-endemic copepod, Tigriopus kingsejongensis
Seunghyun Kang,Do-Hwan Ahn,Jun Hyuck Lee,Sung Gu Lee,Seung Chul Shin,Jungeun Lee,Gi-Sik Min,Hyoungseok Lee,Hyun-Woo Kim,Sanghee Kim,Hyun Park +10 more
TL;DR: The T. kingsejongensis genome provides an interesting example of an evolutionary strategy for Antarctic cold adaptation, and offers new genetic insights into Antarctic intertidal biota.
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Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes
Katsuki Tsuritani,Takuma Irie,Riu Yamashita,Yuta Sakakibara,Hiroyuki Wakaguri,Akinori Kanai,Junko Mizushima-Sugano,Junko Mizushima-Sugano,Sumio Sugano,Kenta Nakai,Yutaka Suzuki +10 more
TL;DR: The data suggest that there are two distinct classes of promoters in humans, with the latter class of promoters emerging frequently during evolution.
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MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors.
Guimin Qin,Saurav Mallik,Ramkrishna Mitra,Aimin Li,Peilin Jia,Christine M. Eischen,Zhongming Zhao +6 more
TL;DR: This study extensively investigated TF and miRNA regulation pairs, their FFLs, and TF-miRNA mediated regulatory networks in two major types of testicular germ cell tumors (TGCT): seminoma (SE) and non-seminoma (NSE).
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The transcriptional repressor HDAC7 promotes apoptosis and c-Myc downregulation in particular types of leukemia and lymphoma.
Bruna Barneda-Zahonero,Olga Collazo,Alba Azagra,I Fernández-Duran,Jordi Serra-Musach,Abul B. M. M. K. Islam,Nerea Vega-García,Roberta Malatesta,Mireia Camós,Antonio Gomez,Lidia Román-González,August Vidal,Nuria Lopez-Bigas,A. Villanueva,Manel Esteller,Maribel Parra +15 more
TL;DR: It is concluded that HDAC7 has a potent anti-oncogenic effect on specific B-cell malignancies, indicating that its deregulation may contribute to the pathogenesis of the disease.
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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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