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EpiFactors: a comprehensive database of human epigenetic factors and complexes

Yulia A. Medvedeva, Andreas Lennartsson, Rezvan Ehsani, Ivan V. Kulakovskiy, Ilya E. Vorontsov, Pouda Panahandeh, Grigory Khimulya, Takeya Kasukawa, Finn Drabløs
2015 Database: The Journal of Biological Databases and Curation  
Here we present EpiFactors, a manually curated database providing information about epigenetic regulators, their complexes, targets and products.  ...  EpiFactors also contains information on 69 protein complexes that are involved in epigenetic regulation.  ...  Acknowledgements The authors are grateful to Anna Palau for her help with the Polycomb group complexes, to Darya Dementieva for her help with the main web-page graphics and to Wyeth Wasserman for gene  ... 
doi:10.1093/database/bav067 pmid:26153137 pmcid:PMC4494013 fatcat:nkcp4onstzcsfkow56etyp2kxy

Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection

Marisol Salgado-Albarrán, Erick I. Navarro-Delgado, Aylin Del Moral-Morales, Nicolas Alcaraz, Jan Baumbach, Rodrigo González-Barrios, Ernesto Soto-Reyes
2021 npj Systems Biology and Applications  
Using integrative analyses of gene co-expression networks and de-novo pathway enrichment, we characterize different gene modules and protein pathways enriched with Transcription Factors or Epifactors relevant  ...  Our results show that targeting the epigenetic machinery could be a feasible alternative to treat COVID-19.  ...  factors (IRF7 and IRF2), cytokines (CCL3, CCL4, and IL1B), and FOS and JUND, members of the AP-1 complex 29 .  ... 
doi:10.1038/s41540-021-00181-x pmid:34031419 fatcat:zidvsnlmrvc2bm3iuwohd4hdwq

Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer

Isaac K. Sundar, Irfan Rahman
2016 American Journal of Physiology - Lung cellular and Molecular Physiology  
Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb.  ...  Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer. modifying enzymes mediate DNA methylation and histone  ...  Michael Bulger and Janice Gerloff for editing the manuscript, and Dr. Dongmei Li at the Clinical and Translational Science Institute, University of Rochester, for biostatistical analyses.  ... 
doi:10.1152/ajplung.00253.2016 pmid:27793800 pmcid:PMC5206398 fatcat:ueipq6ukffc7hhcviuasv7pts4

Transcriptome Architecture of Osteoblastic Cells Infected With Staphylococcus aureus Reveals Strong Inflammatory Responses and Signatures of Metabolic and Epigenetic Dysregulation

Aurélie Nicolas, Martine Deplanche, Pierre-Henri Commere, Alan Diot, Clemence Genthon, Wanderson Marques da Silva, Vasco Azevedo, Pierre Germon, Hélène Jamme, Eric Guédon, Yves Le Loir, Fréderic Laurent (+2 others)
2022 Frontiers in Cellular and Infection Microbiology  
The later included genes coding for components of chromatin-repressive complexes (e.g., NuRD, BAHD1 and PRC1) and epifactors involved in DNA methylation.  ...  Here we present an in-depth analysis of the effect of long-term S. aureus infection on the transcriptional program of human osteoblast-like cells.  ...  Friedrich Götz, (Laboratory of Microbial Genetics, University of Tübingen, Germany) for providing S. aureus mCherrySA113 strain. The authors thank Mary Bret for revising the English.  ... 
doi:10.3389/fcimb.2022.854242 pmid:35531332 pmcid:PMC9067450 fatcat:qhj56ss2zbb53frtr5c5rpj4le

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David Arenillas, Anthony Mathelier, Yulia A. Medvedeva, Andreas Lennartsson, Finn Drabløs (+13 others)
2016 Nucleic Acids Research  
Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FAN-TOM  ...  In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced.  ...  ACKNOWLEDGEMENTS The authors would like to thank all of the members in the FANTOM consortium for fruitful collaboration.  ... 
doi:10.1093/nar/gkw995 pmid:27794045 pmcid:PMC5210666 fatcat:5z6fqqnewbbi7a5mwaipsgmi44

CR2Cancer: a database for chromatin regulators in human cancer

Beibei Ru, Jianlong Sun, Yin Tong, Ching Ngar Wong, Aditi Chandra, Acacia Tsz So Tang, Larry Ka Yue Chow, Wai Lam Wun, Zarina Levitskaya, Jiangwen Zhang
2017 Nucleic Acids Research  
Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining.  ...  We believe that this database would become a valuable resource for cancer epigenetics investigation and potential clinical application. CR2Cancer is freely available at  ...  ACKNOWLEDGEMENTS The authors are grateful to the editor and the anonymous reviewers for their valuable suggestions and comments, which has led to the improvement of this paper.  ... 
doi:10.1093/nar/gkx877 pmid:29036683 pmcid:PMC5753221 fatcat:veidrl3s7fal3kphi2pozb77t4

Network and Evolutionary Analysis of Human Epigenetic Regulators to Unravel Disease Associations

Shinji Ohsawa, Toshiaki Umemura, Tomoyoshi Terada, Yoshinori Muto
2020 Genes  
We carried out a system-level analysis of epigenetic regulators (ERs) and detailed the protein–protein interaction (PPI) network characteristics of disease-associated ERs.  ...  Our analysis of human polymorphism data revealed that genes belonging to DDEN and Seed-DDEN were more likely to show signs of recent positive selection in human history.  ...  We combined the EpiFactors genes, FACER genes, and QuickGO genes to construct a comprehensive list of epigenetic regulators.  ... 
doi:10.3390/genes11121457 pmid:33291839 fatcat:mrdj6i3ojjcfvegz5wojckw46y

Epigenetic and Immune-Cell Infiltration Changes in the Tumor Microenvironment in Hepatocellular Carcinoma

Zeng-Hong Wu, Dong-Liang Yang, Liang Wang, Jia Liu
2021 Frontiers in Immunology  
) were shown to be independent prognostic factors based on lasso regression in the TCGA-LIHC and ICGC databases.  ...  However, a comprehensive review of genomic data was carried out to determine the role of epigenesis in the tumor microenvironment (TME), immune cell-infiltration characteristics in HCC is still insufficient.MethodsThe  ...  We extracted 720 epigenetic-related genes from EpiFactors, a database for epigenetic factors, corresponding genes and products (14) Table S1 .  ... 
doi:10.3389/fimmu.2021.793343 pmid:34925377 pmcid:PMC8674919 fatcat:jesdl3whzrbkbf2c5lkwp3drfq

SWI/SNF Infobase—An exclusive information portal for SWI/SNF remodeling complex subunits

Udayakumar Mani, Alagu Sankareswaran S., Arun Goutham R. N., Suma Mohan S., Fatah Kashanchi
2017 PLoS ONE  
In the current study, a database containing information on the subunits of SWI/SNF-α (BRG1/BRM-Associated Factors (BAF)) and SWI/SNF-β (Polybromo-Associated BAF (PBAF)) sub classes of SWI/SNF family has  ...  A detailed annotation on each subunit, including basic protein/gene information, protein sequence, functional domains, homologs and missense mutations of human proteins have been provided with a user-friendly  ...  We thank Srimari Srikanth for the help in implementation of SVG based cartoons for the database.  ... 
doi:10.1371/journal.pone.0184445 pmid:28961249 pmcid:PMC5621669 fatcat:auc43rsz5bcy5lyymdf42xiege

FusionGDB: fusion gene annotation DataBase

Pora Kim, Xiaobo Zhou
2018 Nucleic Acids Research  
Our analyses identified 331, 303 and 667 in-frame FGs with retaining kinase, DNA-binding, and epigenetic factor domains, respectively, as well as 976 FGs lost protein-protein interaction.  ...  To better understand the function of FGs in cancer types and to promote the discovery of clinically relevant FGs, we built FusionGDB (Fusion Gene annotation DataBase) available at  ...  ACKNOWLEDGEMENTS We thank the members of the Center for Computational Systems Medicine (CCSM) for valuable discussion. We thank Dr. Weiling Zhao for improving the English of the manuscript.  ... 
doi:10.1093/nar/gky1067 pmid:30407583 pmcid:PMC6323909 fatcat:iry6mve4sfhz7pwepm2yb4xkou

SARS-CoV-2 Proteins Exploit Host's Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways

Md. Abdullah-Al-Kamran Khan, Abul Bashar Mir Md. Khademul Islam
2021 Frontiers in Molecular Biosciences  
The constant rise of the death toll and cases of COVID-19 has made this pandemic a serious threat to human civilization.  ...  Moreover, we noticed several presumed infection-induced differentially expressed transcription factors and epigenetic factors, such as miRNAs and several histone modifiers, which can modulate different  ...  Identification of the Host Epigenetic Factors Genes We used EpiFactors database (Medvedeva et al., 2015) to find human genes related to the epigenetic activity.  ... 
doi:10.3389/fmolb.2020.598583 pmid:33585554 pmcid:PMC7872968 fatcat:a2zshhbjlvbqxjzi3gfok55ehy

BAHD1 haploinsufficiency results in anxiety-like phenotypes in male mice

Renaud Pourpre, Laurent Naudon, Hamid Meziane, Goran Lakisic, Luc Jouneau, Hugo Varet, Rachel Legendre, Olivia Wendling, Mohammed Selloum, Caroline Proux, Jean-Yves Coppée, Yann Herault (+2 others)
2020 PLoS ONE  
BAHD1 is a heterochomatinization factor recently described as a component of a multiprotein complex associated with histone deacetylases HDAC1/2.  ...  disorders in a human patient.  ...  Pottier and B. Cayron for breeding mice at the INRAE, T. Sorg and M.C. Birling for the generation of mice at the ICS, and Véronique Douard for helpful discussions.  ... 
doi:10.1371/journal.pone.0232789 pmid:32407325 fatcat:p46b6w6rvvgsta6qit7ufufanu

SARS-CoV-2 proteins exploit host's genetic and epigenetic mediators for the annexation of key host signaling pathways that confers its immune evasion and disease pathophysiology [article]

Md. Abdullah-Al-Kamran Khan, Abul B.M.M.K. Islam
2020 bioRxiv   pre-print
The constant rise of the death toll and cases of COVID-19 has made this pandemic a serious threat to human civilization.  ...  Also, we have shown how host epigenetic factors are involved in the deregulation of gene expression.  ...  We have considered those TFs that are expressed itself and that can 'activate' or 191 'regulated' miRNAs. 192 Identification of the host epigenetic factors genes 193 We used EpiFactors database (Medvedeva  ... 
doi:10.1101/2020.05.06.050260 fatcat:2ynmq4tlazandgnioga7ytgb2u

Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference [article]

Paul J. Hop, René Luijk, Lucia Daxinger, Maarten van Iterson, Koen F. Dekkers, Rick Jansen, Joyce B.J. van Meurs, Peter A.C. 't Hoen, M. Arfan Ikram, Marleen M.J. van Greevenbroek, Dorret I. Boomsma, P. Eline Slagboom (+4 others)
2019 bioRxiv   pre-print
DNA methylation is a key epigenetic modification in human development and disease, yet there is limited understanding of its highly coordinated regulation.  ...  Many of the reported genes were unknown to influence DNA methylation, resulting in a comprehensive resource providing insights in the principles underlying epigenetic regulation.  ...  Core epigenetic factors Next, we compared our findings with a manually curated database of core epigenetic factors (EpiFactors) (Medvedeva et al., 2015) .  ... 
doi:10.1101/823807 fatcat:xsj5jwk2dvghpj3t3a2lsgbdga

Development and validation of a nomogram with an epigenetic signature for predicting survival in patients with lung adenocarcinoma

Jiao Wang, Li He, Yunliang Tang, Dan Li, Yuting Yang, Zhenguo Zeng
2020 Aging  
Epigenetic factors play crucial roles in carcinogenesis by modifying chromatin architecture.  ...  To establish an epigenetic model, we identified prognostic epigenetic regulation-related genes by LASSO and Cox regression analyses, and established a novel 11-gene signature, including EPC1, GADD45A,  ...  FUNDING This work was supported by the National Natural Science Foundation of China (Nos. 81760351 and 81460015).  ... 
doi:10.18632/aging.104090 pmid:33221751 pmcid:PMC7746339 fatcat:swckjgb5v5ehte6jxw6pjw7jci
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