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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Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain.
Aslihan Dincer,David P. Gavin,Ke Xu,Bin Zhang,Joel T. Dudley,Eric E. Schadt,Schahram Akbarian +6 more
TL;DR: Investigation of landscapes of sorted neuronal and non-neuronal nuclei in human postmortem, non-human primate and mouse prefrontal cortex, and blood finds broadest H3K4me3 peaks in human PFC neurons were fully conserved in chimpanzee, macaque and mouse cortical neurons.
Journal ArticleDOI
CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication.
Yang Zhang,Tianyuan Liu,Xuesong Hu,Mei Wang,Jing Wang,Bohao Zou,Puwen Tan,Tianyu Cui,Yiying Dou,Lin Ning,Yan Huang,Shuan Rao,Dong Wang,Xiaoyang Zhao +13 more
TL;DR: Coder et al. as discussed by the authors developed CellCall, a toolkit to infer inter-and intracellular communication pathways by integrating paired ligand-receptor and transcription factor (TF) activity.
Journal ArticleDOI
Modulation of Epidermal Transcription Circuits in Psoriasis: New Links between Inflammation and Hyperproliferation
William R. Swindell,Andrew Johnston,Xianying Xing,John J. Voorhees,James T. Elder,Johann E. Gudjonsson +5 more
TL;DR: A new approach for delineating epidermis-specific pathways and regulatory mechanisms that underlie altered gene expression in psoriasis is developed and highlights previously unrecognized “transcription circuits” that can provide targets for development of non-systemic therapies.
Journal ArticleDOI
Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
Angelika Schmidt,Angelika Schmidt,Francesco Marabita,Francesco Marabita,Narsis A. Kiani,Catharina C. Gross,Henrik J. Johansson,Szabolcs Éliás,Sini Rautio,Matilda Eriksson,Sunjay Jude Fernandes,Gilad Silberberg,Ubaid Ullah,Urvashi Bhatia,Harri Lähdesmäki,Janne Lehtiö,David Gomez-Cabrero,David Gomez-Cabrero,Heinz Wiendl,Riitta Lahesmaa,Jesper Tegnér,Jesper Tegnér +21 more
TL;DR: A novel approach facilitates understanding of the molecular mechanisms underlying iTreg generation as well as of the concomitant changes in the transcriptome and proteome, which has important implications for the treatment of cancer, autoimmune, and inflammatory diseases.
Journal ArticleDOI
Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules.
TL;DR: This work applies a new algorithmic approach for efficient, parameter-free and reproducible identification of network-modules simultaneously across multiple conditions to genome-scale and multi-tissue transcriptomic datasets from rats and humans and identified several common and tissue-specific subnetworks with functional significance, which were not detected by other methods.
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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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