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GTRD: an integrated view of transcription regulation

Semyon Kolmykov, Ivan Yevshin, Mikhail Kulyashov, Ruslan Sharipov, Yury Kondrakhin, Vsevolod J Makeev, Ivan V Kulakovskiy, Alexander Kel, Fedor Kolpakov
2020 Nucleic Acids Research  
The updated version of the GTRD provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities, an integrated genome browser, and  ...  The Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org/) contains uniformly annotated and processed NGS data related to gene transcription regulation: ChIP-seq, ChIP-exo, DNase-seq, MNase-seq  ...  Figure 4 . 4 GTRD -integrated view of transcription regulation. previous publication (35 719 reported in the current release versus 17 485 in the previous one).  ... 
doi:10.1093/nar/gkaa1057 pmid:33231677 fatcat:krekihbvl5hv7pkont2kzepjne

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

Ivan Yevshin, Ruslan Sharipov, Tagir Valeev, Alexander Kel, Fedor Kolpakov
2016 Nucleic Acids Research  
GTRD--Gene Transcription Regulation Database (http://gtrd.biouml.org)--is a database of transcription factor binding sites (TFBSs) identified by ChIPseq experiments for human and mouse.  ...  It provides: (i) browsing and displaying information; (ii) advanced search possibilities, e.g. search of TFBSs near the specified gene or search of all genes potentially regulated by a specified transcription  ...  ACKNOWLEDGEMENTS We thank Ivan Kulakovskiy and Vsevolod Makeev for collaboration between the HOCOMOCO and GTRD databases.  ... 
doi:10.1093/nar/gkw951 pmid:27924024 pmcid:PMC5210645 fatcat:33l6uk5nbvhsddnxktmeloff7m

Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data

Ruslan N. Sharipov, Yury V. Kondrakhin, Anna S. Ryabova, Ivan S. Yevshin, Fedor A. Kolpakov, Roberto Mantovani
2020 PLoS ONE  
Creating a complete picture of the regulation of transcription seems to be an urgent task of modern biology.  ...  Regulation of transcription is a complex process carried out by transcription factors (TFs) and auxiliary proteins.  ...  The key question is to better understand the role of transcription factors (TFs), which regulate the transcriptional machinery in cells.  ... 
doi:10.1371/journal.pone.0243332 pmid:33347457 fatcat:35x7gs2btfaupnc3biyitm6rzm

BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets

Gyan Prakash Mishra, Arup Ghosh, Atimukta Jha, Sunil Kumar Raghav
2020 Frontiers in Genetics  
Thus, there is an ardent need for a comprehensive and user-friendly webserver application that allows the users to either upload multiple datasets or select from the integrated Gene Transcription Regulation  ...  Database (GTRD).  ...  ACKNOWLEDGMENTS We are grateful to the developer of the very efficient tools BEDTOOLS, GTRD, and other tools that we have used to develop our web server tool. We would like to thank Dr.  ... 
doi:10.3389/fgene.2020.00003 pmid:32117432 pmcid:PMC7013082 fatcat:lnhypfzzvfhxdogeo53zbmj52a

Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model

Jiayue-Clara Jiang, Joseph A. Rothnagel, Kyle R. Upton
2021 Scientific Reports  
We have developed a bioinformatic pipeline for the integrated analysis of transcription factor binding and transcriptomic data to identify transposon-derived promoters that are activated in specific diseases  ...  AbstractWhile transposons are generally silenced in somatic tissues, many transposons escape epigenetic repression in epithelial cancers, become transcriptionally active and contribute to the regulation  ...  Acknowledgements We thank the GTRD and ChIP-Atlas databases for compiling ChIP-seq data and making their results publicly available. K.U is supported by NHMRC Fellowship APP1130815.  ... 
doi:10.1038/s41598-021-86395-9 pmid:33850167 fatcat:ekptsdgtkfbhhkq664ahtuat6m

L1PA2 transposons contribute abundant regulatory sequences in MCF7 breast cancer cell line [article]

Jiayue-Clara Jiang, Joe Rothnagel, Kyle R Upton
2020 bioRxiv   pre-print
The ubiquitous and replicative nature of L1PA2 makes them an exemplary vector to disperse co-localised transcription factor binding sites, facilitating the co-ordinated regulation of genes.  ...  We demonstrate that the L1PA2 subfamily is an abundant reservoir of transcription factor binding sites, the majority of which cluster in the LINE1 5′UTR.  ...  While the majority of L1PA2 structures showed a depletion of TFBSs, the 5¢UTR was a prominent reservoir of TFBSs. B) Example GTRD browser view of TFBS distribution in L1PA2 transposons.  ... 
doi:10.1101/2020.09.01.276808 fatcat:gwhbn6oy75dg5jp4htermfwvei

Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity

Atefeh Atefi, Pendar Shojaei Kojouri, Fereshteh Karamali, Shiva Irani, Mohammad Hossein Nasr-Esfahani
2021 BMC Molecular and Cell Biology  
This reporter construct can be used for in vitro monitoring of hRPC identity and verification of an efficient culture medium for maintenance of these cells.  ...  Results For this purpose, after in silico analysis of regulatory regions of human RAX gene, the expression of EGFP reporter derived by putative promoter sequences was first evaluated in 293 T cells and  ...  In order to have a better view of potential regulation of RAX gene at transcriptional level, distal region was also analyzed for putative binding sites of transcription factors involved in retinal progenitor  ... 
doi:10.1186/s12860-021-00378-2 pmid:34348662 pmcid:PMC8335887 fatcat:6hly6rjcjrbkfjndbloxrwztuu

Identification of COVID-19-relevant transcriptional regulatory networks and associated kinases as potential therapeutic targets [article]

Chen Su, Simon Rousseau, Amin Emad
2020 bioRxiv   pre-print
Identification of transcriptional regulatory mechanisms and signaling networks involved in the response of host to infection by SARS-CoV-2 is a powerful approach that provides a systems biology view of  ...  when facing an emerging and novel disease such as COVID-19.  ...  The transcriptional regulatory network (TRN), 35 composed of transcription factors (TFs) and their target genes, play significant roles in regulating these 36 gene expression programs.  ... 
doi:10.1101/2020.12.23.424177 fatcat:xrayh77vrrcqvnw7hcxspklzne

Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection

Peter Ulz, Samantha Perakis, Qing Zhou, Tina Moser, Jelena Belic, Isaac Lazzeri, Albert Wölfler, Armin Zebisch, Armin Gerger, Gunda Pristauz, Edgar Petru, Brandon White (+9 others)
2019 Nature Communications  
Deregulation of transcription factors (TFs) is an important driver of tumorigenesis, but non-invasive assays for assessing transcription factor activity are lacking.  ...  Our approach for mapping tumor-specific transcription factor binding in vivo based on blood samples makes a key part of the noncoding genome amenable to clinical analysis.  ...  In contrast, hematopoietic TFs, such as LYL1, SPIB, and EVI1 (transcriptional regulator ecotropic viral integration site 1 26 (Fig. 2b) had low accessibilities.  ... 
doi:10.1038/s41467-019-12714-4 pmid:31604930 pmcid:PMC6789008 fatcat:dekk3m3j65dlpizoqb2y4unvd4

Introductory Chapter: A Brief Overview of Transcriptional and Post-transcriptional Regulation [chapter]

Kais Ghedira
2018 Transcriptional and Post-transcriptional Regulation  
The PRODORIC2 database hosts one [20] prodoric2.de of the largest collections of DNA- binding sites for prokaryotic transcription factors. Gene Transcription Regulation GTRD http://gtrd.biouml.  ...  Gene regulation has classically been viewed as the interaction between proteins to regulatory elements located at the vicinity of the transcription start site within promoters.  ... 
doi:10.5772/intechopen.79753 fatcat:k3cieiws6jh4pcit7ali3b7zpm

BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data

2019 Nucleic Acids Research  
Due to integration with the Galaxy platform and R/Bioconductor, BioUML provides powerful possibilities for the analyses of omics data.  ...  BioUML (homepage: http://www.biouml.org, main public server: https://ict.biouml.org) is a web-based integrated environment (platform) for systems biology and the analysis of biomedical data generated by  ...  ACKNOWLEDGEMENTS The BioUML team would like to thank all former developers, especially Dr Tagir Valeev and Nikita Tolstykh, for their contribution to the development of the BioUML platform.  ... 
doi:10.1093/nar/gkz440 pmid:31131402 pmcid:PMC6602424 fatcat:qrmgynpm2bcungcd7fsm4lfolm

Genome-Wide Atlas of Promoter Expression Reveals Contribution of Transcribed Regulatory Elements to Genetic Control of Disuse-Mediated Atrophy of Skeletal Muscle

Sergey S. Pintus, Ilya R. Akberdin, Ivan Yevshin, Pavel Makhnovskii, Oksana Tyapkina, Islam Nigmetzyanov, Leniz Nurullin, Ruslan Devyatiyarov, Elena Shagimardanova, Daniil Popov, Fedor A. Kolpakov, Oleg Gusev (+1 others)
2021 Biology  
The developed comprehensive database of transcription of regulatory elements will further stimulate research on the gene regulation of muscle homeostasis in mammals.  ...  We showed that the activation of "shadow" enhancers is tightly linked to specific stages of atrophy and recovery dynamics, with the largest number of specific regulatory elements being transcriptionally  ...  Remarkably, data analysis has identified Mn1, which encodes a transcriptional activator and plays a physiological role in cancer as an up-regulated gene during recovery, while the gene transcript was in  ... 
doi:10.3390/biology10060557 fatcat:r6vyi3wdtfdhtpohb3r2zimfwq

Identification of master regulators in goblet cells and Paneth cells using transcriptomics profiling of gut organoids and multi-layered networks [article]

Agatha Treveil, Padhmanand Sudhakar, Zoe J Matthews, Tomasz Wrzesinski, Emily J Jones, Marton Olbei, Isabelle Hautefort, Lindsay J Hall, Simon R Carding, Ulrike Mayer, Penny P Powell, Tom Wileman (+3 others)
2019 bioRxiv   pre-print
Although transcriptional signatures of intestinal cells have been identified, an integrated and cell type specific network analysis that identifies the key regulators with their disease relevance has been  ...  Conclusions: We describe an integrative organoid study that combines -omics data with multi-layered networks to study the regulatory landscapes of Paneth cells and goblet cells.  ...  Although transcriptional signatures of intestinal cells have been identified, an integrated and cell type specific network analysis that identifies the key regulators with their disease relevance has been  ... 
doi:10.1101/575845 fatcat:rmykkoqtsrh6vgpnm427r5qxze

Effect of fibronectin, FGF-2, and BMP4 in the stemness maintenance of BMSCs and the metabolic and proteomic cues involved

Lingling Chen, Morgan Carlton, Xiaodan Chen, Navdeep Kaur, Hollie Ryan, Tony J Parker, Zhengmei Lin, Yin Xiao, Yinghong Zhou
2021 Stem Cell Research & Therapy  
Fibronectin (FN), fibroblast growth factor 2 (FGF2), and bone morphogenetic protein 4 (BMP4) are the key players in the regulation of stemness and lineage commitment of MSCs.  ...  These results indicate that the culture environment supplemented with the culture cocktail (FN, FGF2, and BMP4) plays an essential role in shaping the pluripotent state of BMSCs.  ...  Acknowledgements The authors would like to acknowledge the scientific and technical assistance of Dr. Pawel Sadowski and Mr.  ... 
doi:10.1186/s13287-021-02227-7 pmid:33676544 fatcat:rgfrip4v6rhjtp5vgfyufwue3q

Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver

Jose P. Silva, Derek van Booven
2018 Scientific Reports  
Here we interrogated whether lncRNA genes may regulate transcription and methylation of their flanking or overlapping protein-coding genes in livers of mice exposed to a 12-week cholesterol-rich Western-style  ...  LncRNAs can increase or decrease expression of protein-coding transcripts in cis 3,5,7 and in trans 8 , through epigenetic, transcriptional and post-transcriptional mechanisms.  ...  We would like to thank Paul Labhart, Active Motif (Carlsbad, California, USA), for assistance with the DNA methylation analyses and critical reading of the manuscript.  ... 
doi:10.1038/s41598-018-29993-4 pmid:30069000 pmcid:PMC6070528 fatcat:nvzqy36wtjbqxb2bijxkc4zdna
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