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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: 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 human DEPhOsphorylation Database DEPOD: 2019 update

2019 Database: The Journal of Biological Databases and Curation  
We report here an update to DEPOD by integrating and/or linking to annotations from 69 other open access databases including disease associations, phosphorylating kinases, protein interactions, and also  ...  The human Dephosphorylation Database (DEPOD) is a manually curated resource that harbors human phosphatases, their protein and non-protein substrates, dephosphorylation sites and the associated signaling  ...  The authors would like to thank the users of DEPOD and colleagues for their feedback (see also the acknowledgments section online).  ... 
doi:10.1093/database/baz133 pmid:31836896 pmcid:PMC6911163 fatcat:gkmqr3epm5bfvb3zxkn3kp26ee

The Comparative Toxicogenomics Database: update 2019

2018 Nucleic Acids Research  
The Comparative Toxicogenomics Database (CTD; is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases  ...  These updates continue to improve CTD and help inform new testable hypotheses about the etiology and mechanisms underlying environmentally influenced diseases.  ...  Here, we provide our biennial database update and describe our newly released chemical-phenotype module, advanced query and display tools for exposure science data, an extensive update to the MEDIC disease  ... 
doi:10.1093/nar/gky868 pmid:30247620 pmcid:PMC6323936 fatcat:4qvewpc42jhsvic7phptfwy6im

SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update

2019 Nucleic Acids Research  
Since its first release, SIGNOR has undergone a significant content increase and the number of annotated causal interactions have almost doubled.  ...  We describe here significant changes in curation policy and a new confidence score, which is assigned to each interaction.  ...  Sev-eral resources collect molecular interaction data as undirected physical protein-protein interactions (MINT, In-tAct, IMEx, BIOGRID) (3) (4) (5) .  ... 
doi:10.1093/nar/gkz949 pmid:31665520 pmcid:PMC7145695 fatcat:aujwealclfgtrawtr3dzap4s4u

APID database: redefining protein–protein interaction experimental evidences and binary interactomes

Diego Alonso-López, Francisco J Campos-Laborie, Miguel A Gutiérrez, Luke Lambourne, Michael A Calderwood, Marc Vidal, Javier De Las Rivas
2019 Database: The Journal of Biological Databases and Curation  
This includes the unification of all the PPIs from five primary databases of molecular interactions (BioGRID, DIP, HPRD, IntAct and MINT), plus the information from two original systematic sources of human  ...  We have performed an update of APID database including a redefinition of several key properties of the PPIs to provide a more precise data integration and to avoid false duplicated records.  ...  an update of the standard format to enable the download and interchange of molecular interaction data (7) .  ... 
doi:10.1093/database/baz005 pmid:30715274 pmcid:PMC6354026 fatcat:jjpl4nnc2retpcta2syx6mamjq

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

RPGeNet v2.0: expanding the universe of retinal disease gene interactions network

2019 Database: The Journal of Biological Databases and Curation  
For the new version, RPGeNet v2.0, the database engine was migrated to Neo4j graph database manager, which speeds up the initial queries and can handle whole interactome data for new ways to query the  ...  RPGeNet integrates interaction information from STRING, BioGRID and PPaxe, along with retina-specific expression data and associated genetic variants, over a Cytoscape.js web interface.  ...  The authors declare that there is no competing interest.  ... 
doi:10.1093/database/baz120 pmid:31712826 pmcid:PMC6846243 fatcat:xyww4zdt5bfwtmlrw5lp74ozqm

iCSDB: an integrated database of CRISPR screens

Ahyoung Choi, Insu Jang, Heewon Han, Min-Seo Kim, Jinhyuk Choi, Jieun Lee, Sung-Yup Cho, Yukyung Jun, Charles Lee, Jaesang Kim, Byungwook Lee, Sanghyuk Lee
2020 Nucleic Acids Research  
Here, we describe iCSDB, an integrated database of CRISPR screening experiments using human cell lines. We compiled two major sources of CRISPR-Cas9 screening: the DepMap portal and BioGRID ORCS.  ...  Furthermore, we have implemented various interactive tools and viewers to facilitate users to choose, examine and compare the screen results both at the gene and guide RNA levels. iCSDB is available at  ...  BioGRID, the database of protein-protein interactions, opened a new dataset of CRISPR phenotype screens (ORCS) that would serve as a data warehouse for the published CRISPR screen results using human,  ... 
doi:10.1093/nar/gkaa989 pmid:33137185 fatcat:od5qi4rlrrcurdsy3tu5prfpdy

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

2019 Nucleic Acids Research  
The 2019 update introduces an extensive technical rewrite making the services faster and more flexible. g:Profiler is freely available at  ...  The results are delivered through an interactive and configurable web design. Results can be downloaded as publication ready visualisations or delimited text files.  ...  Special thanks go to Dmytro Fishman for creating the graphical abstract. We are also grateful to the people in our research group BIIT for their helpful discussions, suggestions and support.  ... 
doi:10.1093/nar/gkz369 pmid:31066453 pmcid:PMC6602461 fatcat:2e4lz222nbgnbb6xinyud4z72u

AraPPINet: An Updated Interactome for the Analysis of Hormone Signaling Crosstalk in Arabidopsis thaliana

Jiawei Zhao, Yu Lei, Jianwei Hong, Cunjian Zheng, Lida Zhang
2019 Frontiers in Plant Science  
Compared to the earlier version, the updated AraPPINet displays a higher accuracy in predicting protein interactions through performance evaluation with independent datasets.  ...  Moreover, network analysis shows that many overlapping proteins are significantly involved in the interactions which mediated the crosstalk among plant hormones.  ...  Database BioGRID IntAct DIP BIND MINT Unique PPIs in total BioGRID 8,953 6,603 95 107 22 8,953 IntAct - 6,861 48 128 30 6,861 DIP - - 146 3 0 146 TABLE 2 | 2 Performance  ... 
doi:10.3389/fpls.2019.00870 pmid:31333706 pmcid:PMC6625390 fatcat:toolppaey5aurnqvofuarc5vrm

How helpful are the protein-protein interaction databases and which ones? [article]

Akhilesh Kumar Bajpai, Sravanthi Davuluri, Kriti Tiwary, Sithalechumi Narayanan, Sailaja Oguru, Kavyashree Basavaraju, Deena Dayalan, Kavitha Thirumurugan, Kshitish K Acharya
2019 bioRxiv   pre-print
Protein-protein interactions (PPIs) are critical, and so are the databases and tools (resources) concerning PPIs.  ...  Overall, hPRINT, STRING and IID together retrieved ~94% of 'total' protein interactions available in the databases. The coverage of certain databases was skewed for some gene-types.  ...  Acknowledgements The authors thank colleagues at BdataA and Shodhaka Life Sciences Pvt. Ltd. for assistance in gathering some of the PPI data and analysis.  ... 
doi:10.1101/566372 fatcat:f46uga34djaarbpao2wgvzldu4

A Framework Integrating Heterogeneous Databases for the Completion of Gene Networks

Han Luo, Donghua Wang, Juan Liu, Ying Ju, Zhe Jin
2019 IEEE Access  
Finally, NIHO infers the interactions among genes by analyzing the proximity scores and adds those interactions that originally not existed into GNs.  ...  In addition, we not only examined the proportion of the added interactions but also observed the performance of NIHO can be promoted when the number of heterogeneous networks is increased.  ...  To show the expansibility of NIHO, we incorporated other databases to predict interactions for BioGRID ( Fig. 6(b) ).  ... 
doi:10.1109/access.2019.2954994 fatcat:yaivz2vxmfcf5ourr456rm477m

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  ...  File 1A), and mining PPI information from IntAct (Orchard et al., 2014) , BioGRID (Oughtred et al., 2019) and DIP (Salwinksi et al., 2004) source databases on a semi-annual update rate.  ... 
doi:10.1093/bioinformatics/btaa1070 pmid:33367505 pmcid:PMC8034533 fatcat:q4tmssyesnaujcabqpvtcpclqq

mPPI: a database extension to visualize structural interactome in a one-to-many manner

Yekai Zhou, Hongjun Chen, Sida Li, Ming Chen
2021 Database: The Journal of Biological Databases and Curation  
Protein–protein interaction (PPI) databases with structural information are useful to investigate biological functions at both systematic and atomic levels.  ...  From the perspective of the display and function of PPI, as well as the structural binding interface, the related database and resources are summarized.  ...  Seventeen databases have been updated since the year 2019, two of which belong to those equipped with the binding interface structure visualization (2, 4, (21) (22) (23) (24) (25) (26) (27) (28) (29)  ... 
doi:10.1093/database/baab036 pmid:34156447 fatcat:jehgi5sty5birgsr6dez3iwr4u

The TargetMine Data Warehouse: Enhancement and Updates

Yi-An Chen, Lokesh P. Tripathi, Takeshi Fujiwara, Tatsuya Kameyama, Mari N. Itoh, Kenji Mizuguchi
2019 Frontiers in Genetics  
coverage of gene-gene relations, small molecule metabolite to pathway mappings, an improved literature survey feature, and in silico prediction of gene functional associations such as protein-protein interactions  ...  Here, we describe the newly modelled biological data types and the enhanced visual and analytical features of TargetMine.  ...  ACKNOWLEDGMENTS The authors thank the members of the Mizuguchi laboratory for their critical review of the study and the manuscript.  ... 
doi:10.3389/fgene.2019.00934 pmid:31649722 pmcid:PMC6794636 fatcat:nkv7njyskjg5xjtie2fmbnvqia
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