دورية أكاديمية
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AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators.

التفاصيل البيبلوغرافية
العنوان: AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators.
المؤلفون: Meiler A; Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany., Marchiano F; Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France., Haering M; Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France., Weitkunat M; Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany., Schnorrer F; Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.; Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France., Habermann BH; Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. bianca.habermann@univ-amu.fr.; Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France. bianca.habermann@univ-amu.fr.
المصدر: Scientific reports [Sci Rep] 2021 Jul 29; Vol. 11 (1), pp. 15463. Date of Electronic Publication: 2021 Jul 29.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : Nature Publishing Group, copyright 2011-
مواضيع طبية MeSH: Epigenomics* , Gene Expression Regulation* , Transcriptome*, Computational Biology/*methods , Data Mining/*methods, Animals ; Caenorhabditis elegans ; Chromatin Immunoprecipitation ; Developmental Biology ; Drosophila ; Epigenesis, Genetic ; Genome ; Histones/chemistry ; Humans ; Internet ; Mice ; Muscle, Skeletal/metabolism ; RNA-Seq ; Software ; Transcription Factors/metabolism ; Transcription, Genetic
مستخلص: Gene expression regulation requires precise transcriptional programs, led by transcription factors in combination with epigenetic events. Recent advances in epigenomic and transcriptomic techniques provided insight into different gene regulation mechanisms. However, to date it remains challenging to understand how combinations of transcription factors together with epigenetic events control cell-type specific gene expression. We have developed the AnnoMiner web-server, an innovative and flexible tool to annotate and integrate epigenetic, and transcription factor occupancy data. First, AnnoMiner annotates user-provided peaks with gene features. Second, AnnoMiner can integrate genome binding data from two different transcriptional regulators together with gene features. Third, AnnoMiner offers to explore the transcriptional deregulation of genes nearby, or within a specified genomic region surrounding a user-provided peak. AnnoMiner's fourth function performs transcription factor or histone modification enrichment analysis for user-provided gene lists by utilizing hundreds of public, high-quality datasets from ENCODE for the model organisms human, mouse, Drosophila and C. elegans. Thus, AnnoMiner can predict transcriptional regulators for a studied process without the strict need for chromatin data from the same process. We compared AnnoMiner to existing tools and experimentally validated several transcriptional regulators predicted by AnnoMiner to indeed contribute to muscle morphogenesis in Drosophila. AnnoMiner is freely available at http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/ .
(© 2021. The Author(s).)
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معلومات مُعتمدة: P40 OD018537 United States OD NIH HHS
المشرفين على المادة: 0 (Histones)
0 (Transcription Factors)
تواريخ الأحداث: Date Created: 20210730 Date Completed: 20211213 Latest Revision: 20211214
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC8322331
DOI: 10.1038/s41598-021-94805-1
PMID: 34326396
قاعدة البيانات: MEDLINE
الوصف
تدمد:2045-2322
DOI:10.1038/s41598-021-94805-1