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Protocols

STRING specifications

Information


Unique identifier OMICS_29032
Name STRING
Alternative name STRINGdb
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Version 10.5
Content license Creative Commons BY 4.0' license
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/STRING

Subtool


  • Viruses.STRING

Documentation


Maintainers


  • person_outline Peer Bork
  • person_outline Lars Juhl Jensen
  • person_outline C. von Mering
  • person_outline Alexander Roth

Additional information


The extension STRING.Viruses can be directly reached at: http://viruses.string-db.org/

Publications for STRING

STRING citations

 (17)
library_books

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity

2018
BMC Genomics
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] d value 0.001. A Venn diagram of protein orthologous groups was constructed with JVenn [].Gene functional annotation (e.g. GO and InterPro terms) and enrichment was found for orthologous groups using StringDB [] and DAVID Bioinformatics resource [, , ].Genome data for BFP (https://www.ncbi.nlm.nih.gov/nuccore/AAXI00000000.1) was downloaded from GenBank []. The BFP scaffold sequences were assembled […]

library_books

Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T PLL

2018
Nat Commun
PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] ally expressed) genes was carried out by Ingenuity Pathway Analysis (IPA, http://www.ingenuity.com/products/ipa), ConsensusPathDB (GSOA), Broad GSEA 2–2.2.1, and KEGG/GO enrichment from the R package STRINGdb, version 9_05.For identification of prognostic GEP signatures, GEPs of T-PLL cases with longest (>800 days, 5 cases) overall survival (OS; time from diagnosis to death of disease; no other ev […]

library_books

Identification of genetic risk factors in the Chinese population implicates a role of immune system in Alzheimer’s disease pathogenesis

2018
Proc Natl Acad Sci U S A
PMCID: 5828602
PMID: 29432188
DOI: 10.1073/pnas.1715554115

[…] p1). We used the R GenABEL package () for data normalization, then mapped the regulatory effects of our candidate variants using R coding and generated network analysis of the top regulatory genes in STRINGdb (). We examined the association of the candidate variants with the plasma and cerebrospinal fluid biomarker data obtained from the ADNI (SI Appendix, SI Materials and Methods). […]

library_books

Preservation Method and Phosphate Buffered Saline Washing Affect the Acute Myeloid Leukemia Proteome

2018
Int J Mol Sci
PMCID: 5796241
PMID: 29351208
DOI: 10.3390/ijms19010296

[…] proteins” refers to the proteins uploaded in WebGestalt): FCpellet/DMSO = ((protein categorypellet/all proteinspellet)/(protein categoryDMSO/all proteinsDMSO)) Regulated proteins were imported into StringDB software version 10.5 for the analysis of protein interactions []. Protein networks were imported to Cytoscape version 3.3.0 []. The MCode plugin was used to identify highly interconnected ne […]

library_books

Regulatory network changes between cell lines and their tissues of origin

2017
BMC Genomics
PMCID: 5596945
PMID: 28899340
DOI: 10.1186/s12864-017-4111-x

[…] or of 652 TFs and 27,175 target genes.To generate the PPI prior, we downloaded Homo sapiens PPI interactions (9606.protein.links.v10.txt.gz) and protein aliases (9606.protein.aliases.v10.txt.gz) from StringDb v10 (2015–10-27). We parsed this PPI data set for the 652 TFs in our TF/target gene prior. To make the PPI prior in the same scale as the regulatory prior, the PPI interaction scores were div […]

call_split

Increased dermal collagen bundle alignment in systemic sclerosis is associated with a cell migration signature and role of Arhgdib in directed fibroblast migration on aligned ECMs

2017
PLoS One
PMCID: 5491269
PMID: 28662216
DOI: 10.1371/journal.pone.0180751
call_split See protocol

[…] Pathway analysis was performed using GOStats package (Ver. 2.38.0) in Bioconductor. Visualization of interactions amongst enriched genes in the collagen bundle alignment signature was performed using STRINGdb. Analysis results of all genes can be found in (). This dataset has been deposited into NCBI’s Gene Expression Omnibus and is accessible through GEO accession number GSE100212. […]

Citations

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STRING institution(s)
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; Centro de Biotecnologia y Genomica de Plantas, Universidad Politécnica de Madrid (UPM)––Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Madrid, Spain; Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark; Resource on Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA, USA; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany; Max Delbruck Centre for Molecular Medicine, Berlin, Germany; Department of Bioinformatics, Biocenter, University of Wurzburg, Wurzburg, Germany
STRING funding source(s)
Supported by the Danish Council for Independent Research (DFF-4005-00443), the National Institutes of Health (NIH) Illuminating the Druggable Genome Knowledge Management Center (U54 CA189205 and U24 224370), the NIH (NIGMS P41 GM103504), by grant number 2018- 183120 from the Chan Zuckerberg Initiative DAF, and the Silicon Valley Community Foundation.

STRING reviews

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