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Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

Sushil Tripathi, Steven Vercruysse, Konika Chawla, Karen R. Christie, Judith A. Blake, Rachael P. Huntley, Sandra Orchard, Henning Hermjakob, Liv Thommesen, Astrid Lægreid, Martin Kuiper
2016 Database: The Journal of Biological Databases and Curation  
We demonstrate this with a project in which we mobilize biological domain experts who curate large amounts of DNA binding transcription factors, and show that they, although new to the field of curation  ...  We argue how cooperation between the scientific community and professional curators can increase the capacity of capturing precise knowledge from literature.  ...  Acknowledgements We thank Tony Sawford for assistance and guidance in submitting DbTF-annotations to the GO database, and Marine Dumousseau and Maximilian Koch for assistance and guidance in submitting DbTF-target gene  ... 
doi:10.1093/database/baw088 pmid:27270715 pmcid:PMC4911790 fatcat:bgvk2mjfxrcinmhz5jykd3cotq

The Gene Regulation Knowledge Commons

Martin Kuiper, Joseph Bonello, Jesualdo Tomás Fernández-Breis, Philipp Bucher, Matthias E. Futschik, Pascale Gaudet, Ivan V. Kulakovskiy, Luana Licata, Colin Logie, Ruth C. Lovering, Vsevolod J. Makeev, Sandra Orchard (+75 others)
2021 Biochimica et Biophysica Acta. Gene Regulatory Mechanisms  
The COST Action Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC, CA15205, organized nine workshops in a four-year period, starting September 2016.  ...  knowledge management workflows, encourage new experimental approaches and thoroughly involve end-users in the process to design the Gene Regulation Knowledge Commons (GRKC).  ...  The European Cooperation in Science and Technology (COST) Action Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) is the result of an initiative which started in 2013: The Gene Regulation  ... 
doi:10.1016/j.bbagrm.2021.194768 pmid:34757206 fatcat:gkal73srhnfzloesoiattmxcxm

Common themes in microbial pathogenicity revisited

B B Finlay, S Falkow
1997 Microbiology and Molecular Biology Reviews  
Several common themes again are employed, including antigenic variation, camouflage by binding host molecules, and enzymatic degradation of host immune components.  ...  These common themes are found throughout bacterial virulence factors. For example, there are only a few general types of toxins, despite a large number of host targets.  ...  protein to bind to specific DNA sequences, which initiates the transcription of genes that contain a conserved upstream regulator-binding sequence.  ... 
pmid:9184008 pmcid:PMC232605 fatcat:mgzp3s73mvfi5ojh65rhqyoifq

Common themes in microbial pathogenicity

B B Finlay, S Falkow
1989 Microbiological reviews  
Because pathogens must overcome similar host barriers, common themes in microbial pathogenesis have evolved.  ...  Highly adapted pathogenic organisms have developed biochemical sensors exquisitely designed to measure and respond to such environmental stimuli and accordingly to regulate a cascade of virulence determinants  ...  Recent data indicate that this region encodes a 30-kDa positive regulator which controls transcriptional expression of the ipaB, ipaC, and ipaD genes as well as another genetic cluster, i'irG; the lirF  ... 
pmid:2569162 pmcid:PMC372728 fatcat:bgcw6uf65zhn7epsa27fcjnrnq

Commons, Anticommons, and Community in Biotechnological Assets

Stephen R Munzer
2008 Theoretical Inquiries in Law  
The hope is most realistic in the case of the BIOS patent-based commons. The members of BIOS are a community. This community can generate scientific knowledge (T2).  ...  regulation of transcription "involves the interplay of multiple components." 41 As to replication, new data and analysis suggest "that largerscale chromosomal architecture may be more important than the  ... 
doi:10.2202/1565-3404.1216 fatcat:w5honmb56zeedgnxiqhsbjkxvm

Identification of Common Differentially Expressed Genes in Urinary Bladder Cancer

Apostolos Zaravinos, George I. Lambrou, Ioannis Boulalas, Dimitris Delakas, Demetrios A. Spandidos, Michael Polymenis
2011 PLoS ONE  
Genes manifested various differential patterns of expression, based on PCA. YY1 and NFkB were among the most common transcription factors that regulated the expression of the identified DE genes.  ...  GO analysis revealed the prevalence of transport and binding genes in the common down-regulated DE genes; the prevalence of RNA metabolism and processing genes in the up-regulated DE genes; as well as  ...  The TRANSFAC transcription factor database was used for the identification of gene transcription factor binding sites [34] .  ... 
doi:10.1371/journal.pone.0018135 pmid:21483740 pmcid:PMC3070717 fatcat:ctsqatrfxfbplhod3bqhjb6xvu

Epilepsy: A Common Co-Morbidity in ASD [chapter]

Shaheen Akhter
2021 Autism - Heterogeneity Etiological Core and Outcome [Working Title]  
of some common underlying pathophysiologic mechanisms.  ...  The fact that multiple genetic and epigenetic factors, metabolic diseases, environmental factors and epileptic encephalopathies are related to the causation of both ASD and epilepsy indicate the presence  ...  Knowledge of copy number variation and single gene disorders that are disturbed in these two developmental disorders include gene transcriptional regulation; cellular growth and proliferation; and synapse  ... 
doi:10.5772/intechopen.96484 fatcat:vyjt5euiibghlgjbby54il4wfq

Genetic Landscape of Common Epilepsies: Advancing towards Precision in Treatment

Sarita Thakran, Debleena Guin, Pooja Singh, Priyanka Singh, Samiksha Kukal, Chitra Rawat, Saroj Yadav, Suman S. Kushwaha, Achal K. Srivastava, Yasha Hasija, Luciano Saso, Srinivasan Ramachandran (+1 others)
2020 International Journal of Molecular Sciences  
This review aims to comprehensively present a state-of-art review of all the genes and their genetic variants that are associated with all common epilepsy subtypes.  ...  It also encompasses the basis of these genes in the epileptogenesis.  ...  A 68bp tandem repeat element containing binding site for AP-1 transcription factor, is present in the core promoter of PDYN gene, and regulate its expression [206] .  ... 
doi:10.3390/ijms21207784 pmid:33096746 pmcid:PMC7589654 fatcat:6dzny36blrgp7nvkxwwqahzdv4

The vertebrate Embryo Clock: Common players dancing to a different beat

Gil Carraco, Ana P. Martins-Jesus, Raquel P. Andrade
2022 Frontiers in Cell and Developmental Biology  
This review aims to summarize the available knowledge regarding the pace of the EC, its regulation and experimental manipulation and to expose new questions that might help shed light on what is still  ...  The discovery of a molecular Embryo Clock (EC) underlying the periodicity of somite formation shed light on the importance of gene expression dynamics for pattern formation.  ...  Acknowledgments The authors are grateful for the careful analysis and critical discussion with the reviewers that greatly improved our final manuscript.  ... 
doi:10.3389/fcell.2022.944016 pmid:36036002 pmcid:PMC9403190 fatcat:pk7v5f5o7zbxzoktk4hdy5wrji

Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes

Samantha N. Piekos, Sadhana Gaddam, Pranav Bhardwaj, Prashanth Radhakrishnan, Ramanathan V. Guha, Anthony E. Oro, Ilya Ioshikhes
2021 PLoS Computational Biology  
We have addressed this issue through the creation of Biomedical Data Commons (BMDC), a knowledge graph that integrates data from multiple sources into a single queryable format.  ...  This is particularly true for Type 1 Diabetes (T1D), one of the most intensely studied common childhood diseases.  ...  We acknowledge that we used publicly available information from the National Library of Medicine in this work.  ... 
doi:10.1371/journal.pcbi.1009382 pmid:34543288 pmcid:PMC8483327 fatcat:76h55gtz3jghlnfn5lx6j4vj2i

Systematic evaluation of the effect of common SNPs on pre-mRNA splicing

Abdou ElSharawy, Bernd Hundrieser, Mario Brosch, Michael Wittig, Klaus Huse, Matthias Platzer, Albert Becker, Matthias Simon, Philip Rosenstiel, Stefan Schreiber, Michael Krawczak, Jochen Hampe
2009 Human Mutation  
The methodology of the present study was careful to avoid bias against certain candidate genes.  ...  proteome and regulation of gene expression in higher eukaryotes.  ...  Frank Kempken from the Botanical Institute of the Christian-Albrechts University of Kiel for taking on the role of my official supervisor in the Faculty of Mathematics and Natural Sciences.  ... 
doi:10.1002/humu.20906 pmid:19191320 fatcat:ue2ninlicrd2jkbgta4fb3sywq

Deletions at the chromosome 3 common eliminated region 1 on 3p21.3 in human breast tumors

ThE Petursdottir, U Thorsteinsdottir, JG Jonasson, PH Moller, C Huiping, J Bjornsson, V Egilsson, S Imreh, S Ingvarsson
2005 Breast Cancer Research  
These interactions probably involve autocrine and paracrine action of multiple growth factors, including members of the TGF-β family, which are expressed in both stroma and epithelium.  ...  Studies of human tumors have demonstrated inactivating mutations in human tumors of genes encoding proteins involved in TGF-β signal transduction, including DPC4/Smad4, Smad2, and the type II TGF-β receptor  ...  Genes are regulated by multiple transcription binding sites that interact with a specific S49 combination of transcription factors.  ... 
doi:10.1186/bcr1139 fatcat:kkoevwwrzzc4tlli6c4s5v5gky

Genetic basis of common human disease: insight into the role of nonsynonymous SNPs from genome-wide association studies

Lipika R Pal, John Moult
2011 Genome Biology  
I3 Are clinical genomes already becoming semi-routine for patient care?  ...  purifying selection in shaping patterns of proteincoding variation and the diff erential signatures of population structure from rare and common variation.  ...  novo copy number variation, de novo point mutations of large eff ect could explain the majority of all mental retardation cases in the population.  ... 
doi:10.1186/gb-2011-12-s1-p10 fatcat:2c4ketwxg5bt7ge3pk3xfdwfae

Rare and Common Genetic Events in Type 2 Diabetes: What Should Biologists Know?

Amélie Bonnefond, Philippe Froguel
2015 Cell Metabolism  
enabling the careful assessment of hundreds of thousands of common SNPs in a large sample size of T2D cases and controls.  ...  PDX1 encodes a transcription factor with a key role in pancreatic beta cell development, and mutations in this gene cause MODY-4 or neonatal diabetes associated with pancreatic agenesis when mutations  ... 
doi:10.1016/j.cmet.2014.12.020 pmid:25640731 fatcat:7qvb3isjm5e73lnbxv32qvjoay

Gene Ontology representation for transcription factor functions

Pascale Gaudet, Colin Logie, Ruth C. Lovering, Martin Kuiper, Astrid Lægreid, Paul D. Thomas
2021 Biochimica et Biophysica Acta. Gene Regulatory Mechanisms  
We distinguish between three classes of activities involved in transcription or directly regulating it - general transcription factors, DNA-binding transcription factors, and transcription co-regulators  ...  The Gene Ontology (GO) provides a rigorously defined set of concepts that describe the functions of gene products.  ...  Acknowledgements We thank many GREEKC and GO consortium members for useful discussions that led to the development of these guidelines, in particular Marcio L.  ... 
doi:10.1016/j.bbagrm.2021.194752 pmid:34461313 fatcat:cctwtqy64ja7xoiiffrpocqoq4
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