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The BioGRID interaction database: 2013 update

Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Sven Heinicke, Lorrie Boucher, Andrew Winter, Chris Stark, Julie Nixon, Lindsay Ramage, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Ashton Breitkreutz (+8 others)
2012 Nucleic Acids Research  
This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update.  ...  The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions  ...  ACKNOWLEDGEMENTS The authors thank Chris Grove, Paul Sternberg and Anastasia Baryshnikova for ongoing collaborative development of the Genetic Interaction Structured Terminology.  ... 
doi:10.1093/nar/gks1158 pmid:23203989 pmcid:PMC3531226 fatcat:nmn2ijk3qje6jfpsgpzgk2p2nm

The BioGRID interaction database: 2019 update

Rose Oughtred, Chris Stark, Bobby-Joe Breitkreutz, Jennifer Rust, Lorrie Boucher, Christie Chang, Nadine Kolas, Lara O'Donnell, Genie Leung, Rochelle McAdam, Frederick Zhang, Sonam Dolma (+5 others)
2018 Nucleic Acids Research  
The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the curation and archival storage of protein, genetic and chemical interactions  ...  BioGRID now captures chemical interaction data, including chemical-protein interactions for human drug targets drawn from the DrugBank database and manually curated bioactive compounds reported in the  ...  ACKNOWLEDGEMENTS The authors thank John Aitchison, Brenda Andrews, Gary Bader, Anastasia Baryshnikova  ... 
doi:10.1093/nar/gky1079 pmid:30476227 pmcid:PMC6324058 fatcat:72ppbdg3vbbhzfeugxmqu7athm

The BioGRID interaction database: 2015 update

Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Rose Oughtred, Lorrie Boucher, Sven Heinicke, Daici Chen, Chris Stark, Ashton Breitkreutz, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Julie Nixon (+10 others)
2014 Nucleic Acids Research  
This interaction count represents a 50% increase compared to our previous 2013 BioGRID update.  ...  The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein in- teractions curated from the primary biomedical  ...  ACKNOWLEDGEMENTS The authors thank Chris Grove and Paul Sternberg at WormBase for ongoing collaborative development of the Genetic Interaction Ontology. We also thank Mike Cherry  ... 
doi:10.1093/nar/gku1204 pmid:25428363 pmcid:PMC4383984 fatcat:jeok6meldzhmphu3mpxqxpeoiy

The ConsensusPathDB interaction database: 2013 update

Atanas Kamburov, Ulrich Stelzl, Hans Lehrach, Ralf Herwig
2012 Nucleic Acids Research  
ConsensusPathDB has grown mainly due to the integration of 12 further databases; it now contains 215 541 unique interactions and 4601 pathways from overall 30 databases.  ...  In this update article, we report its significant progress in terms of interaction content and web interface tools.  ...  ACKNOWLEDGEMENTS We are grateful to the developers of all source databases who have provided interaction data to the public domain.  ... 
doi:10.1093/nar/gks1055 pmid:23143270 pmcid:PMC3531102 fatcat:uppbce2ezjfpdb53edgzg4a34m

Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions

Rose Oughtred, Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Christie S. Chang, Jennifer M. Rust, Chandra L. Theesfeld, Sven Heinicke, Ashton Breitkreutz, Daici Chen, Jodi Hirschman, Nadine Kolas, Michael S. Livstone (+10 others)
2016 Cold Spring Harbor Protocols  
The BioGRID database is an extensive repository of curated genetic and protein interactions for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and the yeast Candida  ...  viewer, and how to download data files for either selected interactions or the entire BioGRID interaction data set.  ...  ACKNOWLEDGMENTS The authors thank Chris Grove and Paul Sternberg at WormBase for ongoing collaborative development of the Genetic Interaction Ontology.  ... 
doi:10.1101/pdb.prot088880 pmid:26729909 pmcid:PMC5975959 fatcat:ublifsrndreuhomte4g7527r2e

GeneMANIA Prediction Server 2013 Update

Khalid Zuberi, Max Franz, Harold Rodriguez, Jason Montojo, Christian Tannus Lopes, Gary D. Bader, Quaid Morris
2013 Nucleic Acids Research  
ACKNOWLEDGEMENTS We thank Gabe Musso for zebrafish data; Mohan Babu, Sadhna Phanse and Roland Arnold for E. coli data; members of the Morris and Bader labs, especially Ron Ammar and Scott Zuyderduyn, for  ...  Our front page provides up-to-date statistics on the number of interactions and networks in our database.  ...  /PubMed link and GEO link for co-expression data, protein interaction database for physical interaction data.  ... 
doi:10.1093/nar/gkt533 pmid:23794635 pmcid:PMC3692113 fatcat:qcxb5ixypjb23f4jkktiauhogq

The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update

I. Sadowski, B.-J. Breitkreutz, C. Stark, T.-C. Su, M. Dahabieh, S. Raithatha, W. Bernhard, R. Oughtred, K. Dolinski, K. Barreto, M. Tyers
2013 Database: The Journal of Biological Databases and Curation  
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update.  ...  All records are cross-referenced with the BioGRID interaction database (2), the Saccharomyces Genome Database (SGD) (4) and the NCBI protein database (5) , and hyperlinks are provided to original articles  ...  Author(s) 2013.  ... 
doi:10.1093/database/bat026 pmid:23674503 pmcid:PMC3653121 fatcat:owoc7slcjrhedcrl427zafbrju

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

Jing Wang, Dexter Duncan, Zhiao Shi, Bing Zhang
2013 Nucleic Acids Research  
The current version of WebGestalt supports 8 organisms and 201 gene identifiers from various databases and different technology platforms, making it directly available to the fast growing omics community  ...  Finally, new interactive features, such as pathway map, hierarchical network visualization and phenotype ontology visualization have been added to WebGestalt to help users better understand the enrichment  ...  ACKNOWLEDGEMENTS This work was conducted in part using the resources of the Advanced Computing Center for Research and Education at Vanderbilt University, Nashville, TN.  ... 
doi:10.1093/nar/gkt439 pmid:23703215 pmcid:PMC3692109 fatcat:umqgbynhazf3nja6bkeejf2ekq

Measuring pathway database coverage of the phosphoproteome

Hannah Huckstep, Liam G. Fearnley, Melissa J. Davis
2021 PeerJ  
We first determined the global coverage of each database at both the protein and phosphosite level.  ...  Finally, we looked in detail at the coverage of each database over six experimental datasets.  ...  ACKNOWLEDGEMENTS The authors thank Daniel Esposito, Samuel Lee and Dharmesh Bhuva for technical support. ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj.11298 pmid:34113485 pmcid:PMC8162239 fatcat:yx4zibz3cvcm7h344ie3g2ge5u

CHD@ZJU: a knowledgebase providing network-based research platform on coronary heart disease

Leihong Wu, Xiang Li, Jihong Yang, Yufeng Liu, Xiaohui Fan, Yiyu Cheng
2013 Database: The Journal of Biological Databases and Curation  
Additionally, CHD@ZJU incorporated the protein-protein interactions to investigate the cross-talk within the pathways from a multi-layer network view.  ...  Almost half of the genes collected in CHD@ZJU were novel to other publicly available CHD databases.  ...  The information about PPI interactions with ABCA1 was displayed with related references and interaction types from HPRD and BioGRID Databases.  ... 
doi:10.1093/database/bat047 pmid:23818526 pmcid:PMC3697781 fatcat:ccedcmva2ffxhfqst5een3t5me

The YeastGenome app: the Saccharomyces Genome Database at your fingertips

Edith D. Wong, Kalpana Karra, Benjamin C. Hitz, Eurie L. Hong, J. Michael Cherry
2013 Database: The Journal of Biological Databases and Curation  
The authors also thank the Saccharomyces Genome Database project staff, especially Maria Costanzo, for testing of the app and editing of this article. Conflict of interest. None declared.  ...  Acknowledgements The authors wish to acknowledge the eager alpha-and beta-testers of YeastGenome for taking the time to test the app and share with us their feedback and wish lists.  ...  Updates of the data in the database will be released regularly, with or without software updates, through the iTunes App Store.  ... 
doi:10.1093/database/bat004 pmid:23396302 pmcid:PMC3567487 fatcat:gsn4teoftjghjnfxl4xd73jj64

GeneStoryTeller: a mobile app for quick and comprehensive information retrieval of human genes

Stergiani V. Eleftheriou, Marilena M. Bourdakou, Emmanouil I. Athanasiadis, George M. Spyrou
2015 Database: The Journal of Biological Databases and Curation  
available databases, as a summary story.  ...  The most challenging part during the development of the GeneStoryTeller was to keep balance between storing data locally within the app and obtaining the updated content dynamically via a network connection  ...  /) (6) and (iii) PathWayCommons (www.pathwaycom-mons.org/) (7), (iv) the protein-protein interaction repository Biogrid (http://thebiogrid.org/) (8), (v) the Drug-Gene Interaction database DGIdb (http:  ... 
doi:10.1093/database/bav048 pmid:26055097 pmcid:PMC4460399 fatcat:j2iyqpovhbcsfk3egknh4xryhu

PICKLE 3.0: Enriching the human Meta-database with the mouse protein interactome extended via mouse-human orthology

Georgios N Dimitrakopoulos, Maria I Klapa, Nicholas K Moschonas, Pier Luigi Martelli
2020 Bioinformatics  
Summary The PICKLE 3.0 upgrade refers to the enrichment of this human protein-protein interaction (PPI) meta-database with the mouse protein interactome.  ...  The relational scheme of PICKLE 3.0 has been amended to exploit the Mouse Genome Informatics (MGI) mouse-human ortholog gene pair collection, enabling (i) the extension through orthology of the mouse interactome  ...  Introduction Protein InteraCtion KnowLegdE (PICKLE) meta-database has been developed to consistently integrate primary human PPI datasets (Gioutlakis et al, 2017; Klapa et al, 2013) .  ... 
doi:10.1093/bioinformatics/btaa1070 pmid:33367505 pmcid:PMC8034533 fatcat:q4tmssyesnaujcabqpvtcpclqq

IQdb: an intelligence quotient score-associated gene resource for human intelligence

Lei Kong, Lu Cheng, Li-ya Fan, Min Zhao, Hong Qu
2013 Database: The Journal of Biological Databases and Curation  
Database URL: http://IQdb.cbi.pku.edu.cn.  ...  Based on the core dataset and 46 confirmed linked genomic regions, more than 6932 potential IQ-related genes are expanded using data of protein-protein interactions.  ...  And 3063 genes that interacted with 158 genes in the core dataset were further introduced from the BioGRID (9), HPRD (10) and BIND (11) databases.  ... 
doi:10.1093/database/bat063 pmid:24030781 pmcid:PMC3770929 fatcat:iak7yt3ynvdebon6pamkemp3tq

4DGenome: a comprehensive database of chromatin interactions

Li Teng, Bing He, Jiahui Wang, Kai Tan
2015 Bioinformatics  
Records in the database are described using a standardized file format, facilitating data exchange. The vast major of the interactions were assigned a confidence score.  ...  Results: We describe the 4DGenome database that stores chromatin interaction data compiled through comprehensive literature curation.  ...  Acknowledgements We thank members of the Tan lab for helpful discussion.  ... 
doi:10.1093/bioinformatics/btv158 pmid:25788621 pmcid:PMC4514924 fatcat:457an7nmdzcjtly2tg3ffihzum
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