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TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins

U. Schaefer, S. Schmeier, V. B. Bajic
2010 Nucleic Acids Research  
We have developed the Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins (TcoF-DB). A web-based interface for this resource can be freely accessed at  ...  Proteins that interact with TFs in the context of transcription regulation but do not bind to the DNA themselves, we consider transcription co-factors (TcoFs).  ...  With this in mind, we developed a public resource: Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins (TcoF-DB).  ... 
doi:10.1093/nar/gkq945 pmid:20965969 pmcid:PMC3013796 fatcat:hvj66s2arvf45mr5hnuo25y5ji

DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining

Adil Salhi, Magbubah Essack, Tanvir Alam, Vladan P. Bajic, Lina Ma, Aleksandar Radovanovic, Benoit Marchand, Sebastian Schmeier, Zhang Zhang, Vladimir B. Bajic
2017 RNA Biology  
genes and proteins, drug indications and side effects, mutations, diseases, etc.  ...  Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human  ...  Acknowledgments The computational analysis for this study was performed on Dragon  ... 
doi:10.1080/15476286.2017.1312243 pmid:28387604 pmcid:PMC5546543 fatcat:oqsxpxkigzbmlazrpvqot5ytsi

Network analysis of microRNAs and their regulation in human ovarian cancer

Sebastian Schmeier, Ulf Schaefer, Magbubah Essack, Vladimir B Bajic
2011 BMC Systems Biology  
Unfortunately, the specific machinery of miRNA regulation, involving transcription factors (TFs) and transcription co-factors (TcoFs), is not well understood.  ...  Results: We analysed experimentally verified data from multiple sources that describe miRNA influence on diseases, miRNA targeting of mRNAs, and on protein-protein interactions, and combined this data  ...  Acknowledgements None Authors' contributions SS, US, and VBB conceptualised the study. SS, US, and ME collected and integrated the data, performed the analysis, and wrote the manuscript.  ... 
doi:10.1186/1752-0509-5-183 pmid:22050994 pmcid:PMC3219655 fatcat:r7463u5jyzbqfm2irx6xbvjbsy

FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

Tanvir Alam, Mahmut Uludag, Magbubah Essack, Adil Salhi, Haitham Ashoor, John B. Hanks, Craig Kapfer, Katsuhiko Mineta, Takashi Gojobori, Vladimir B. Bajic
2016 Nucleic Acids Research  
Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are  ...  In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue.  ...  ACKNOWLEDGEMENTS The computational analysis for this study was performed on Dragon and Snapdragon compute clusters of Computational Bioscience Research Center at King Abdullah University of Science and  ... 
doi:10.1093/nar/gkw973 pmid:27924038 pmcid:PMC5389649 fatcat:snmdgtjalffhzcdjzifwmgfayq

Pharmacological manipulation of transcription factor protein-protein interactions: opportunities and obstacles

Frank Fontaine, Jeroen Overman, Mathias François
2015 Cell Regeneration  
Yet, very little is known about the molecular modalities of highly dynamic interactions between transcription factors, genomic DNA, and protein partners.  ...  Transcription factors, known to act mostly via protein-protein interaction, may well be at the forefront of this type of drug development.  ...  All authors read and approved the final manuscript.  ... 
doi:10.1186/s13619-015-0015-x pmid:25848531 pmcid:PMC4365538 fatcat:uaprnuxptvakbnfhmygb5lhs64

A comprehensive manually-curated compendium of bovine transcription factors

Marcela M. de Souza, Adhemar Zerlotini, Ludwig Geistlinger, Polyana C. Tizioto, Jeremy F. Taylor, Marina I. P. Rocha, Wellison J. S. Diniz, Luiz L. Coutinho, Luciana C. A. Regitano
2018 Scientific Reports  
Protoc., Schaefer,U., Schmeier,S. and Bajic,V.B. (2011) TcoF-DB: Dragon database for human 5 3 3 transcription co-factors and transcription factor interacting proteins.  ...  We extracted protein interaction data from the IntAct database for all proteins that interacted 2 5 0 with the bovine TFs, which resulted in 31,799 interactions.  ...  The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/254011 doi: bioRxiv preprint first posted online Jan. 27, 2018;  ... 
doi:10.1038/s41598-018-32146-2 pmid:30213987 pmcid:PMC6137171 fatcat:42drieopnfabbpllyb3fatlcc4

A comprehensive manually-curated Compendium of Bovine Transcription Factors [article]

Marcela Maria de Souza, Juan Manuel Vaquerizas, Adhemar Zerlotini, Ludwig Geistlinger, Benjamín Hernández-Rodríguez, Polyana Tizioto, Jeremy F Taylor, Marina Ibelli Rocha, Wellison Jarles Diniz, Luiz Coutinho, Luciana Correia de Almeida Regitano
2018 bioRxiv   pre-print
Transcription factors (TFs) are pivotal regulatory proteins that control gene expression in a context-dependent and tissue-specific manner.  ...  In addition, we provide a list of putative transcription cofactors derived from known interactions with the identified TFs.  ...  Protoc., Schaefer,U., Schmeier,S. and Bajic,V.B. (2011) TcoF-DB: Dragon database for human 5 3 3 transcription co-factors and transcription factor interacting proteins.  ... 
doi:10.1101/254011 fatcat:jx35fdv6arg7lllampw7xpfr3q

AN1-type zinc finger protein 3 (ZFAND3) is a transcriptional regulator that drives Glioblastoma invasion

Anne Schuster, Eliane Klein, Virginie Neirinckx, Arnon Møldrup Knudsen, Carina Fabian, Ann-Christin Hau, Monika Dieterle, Anais Oudin, Petr V. Nazarov, Anna Golebiewska, Arnaud Muller, Daniel Perez-Hernandez (+7 others)
2020 Nature Communications  
Our findings indicate that ZFAND3 acts within a nuclear protein complex to activate gene transcription and regulates the promoter of invasion-related genes such as COL6A2, FN1, and NRCAM.  ...  Here, we use a genome-wide interference screen to determine invasion-essential genes and identify the AN1/A20 zinc finger domain containing protein 3 (ZFAND3) as a crucial driver of GBM invasion.  ...  Data availability All data generated or analysed during this study are included in this published article (and its Supplementary Data files).  ... 
doi:10.1038/s41467-020-20029-y pmid:33311477 fatcat:7qhocnzulbhcplq2zyspvoap5m

An endoribonuclease-based incoherent feedforward loop for decoupling resource-limited genetic modules [article]

Ross D Jones, Yili Qian, Breanna DiAndreth, Velia Siciliano, Jin Huh, Ron Weiss, Domitilla Del Vecchio
2019 bioRxiv   pre-print
A significant goal of synthetic biology is to develop genetic devices for accurate and robust control of gene expression.  ...  Our resource competition characterization along with the feedforward control device will be critical for achieving robust and accurate controlof gene expression  ...  TcoF-DB: Dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Research 39, 106-110 (2011). 42. Poss, Z. C., Ebmeier, C. C. & Taatjes, D. J.  ... 
doi:10.1101/867028 fatcat:kscee6pujnfinl5b2p3h7csphe

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

Christopher S. Smillie, Moshe Biton, Jose Ordovas-Montanes, Keri M. Sullivan, Grace Burgin, Daniel B. Graham, Rebecca H. Herbst, Noga Rogel, Michal Slyper, Julia Waldman, Malika Sud, Elizabeth Andrews (+21 others)
2019 Cell  
Our work provides a framework for interrogating complex human diseases and mapping risk variants to cell types and pathways.  ...  Inflammatory fibroblasts, inflammatory monocytes, microfold-like cells, and T cells that co-express CD8 and IL-17 expand with disease, forming intercellular interaction hubs.  ...  TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res. 39, D106-D110.  ... 
doi:10.1016/j.cell.2019.06.029 pmid:31348891 pmcid:PMC6662628 fatcat:t2pihb74ofglvcn7pq2rnwp2dq