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Genes2Networks specifications

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Unique identifier OMICS_03952
Name Genes2Networks
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Publication for Genes2Networks

Genes2Networks in publications

 (7)
PMCID: 5820528
PMID: 29503661
DOI: 10.3389/fgene.2018.00042

[…] web interface (https://amp.pharm.mssm.edu/x2k/; chen et al., ). x2k identifies the enriched transcription factors (tfs) from the upstream of the shared degs using a chea database (chen et al., ). genes2networks (g2n) module of x2k connects tfs with ppi to yield transcriptional complexes related to these gene signatures. protein kinases responsible for tf complex formation and functional […]

PMCID: 4450512
PMID: 25951516
DOI: 10.7554/eLife.07186.020

[…] matrix, and euclidean distance was used as a distance metric for hierarchical clustering. ppi networks were constructed using the expression2kinase software () based on an updated version of genes2networks (), only direct connections (path length = 1) were considered, and all published ppi databases except predicted ppis were included. networks were visualized and formatted in yed […]

PMCID: 3702487
PMID: 23803348
DOI: 10.1186/1752-0509-7-51

[…] products of genes do not act alone but rather cooperate with other proteins to perform a function, we assessed the protein-protein interactions (ppis) of the focal 329 genes. for this we used genes2networks, which integrates the data contained in multiple interaction network datasets, enables the user to determine the path length (degree of interaction), and incorporates possible […]

PMCID: 3321097
PMID: 22406746
DOI: 10.1038/nm.2685

[…] for the pattern of gene expression in the tg26 kidney., we linked these tfs to upstream regulatory mechanisms by constructing a protein-protein interaction subnetwork based on known interactions (genes2networks). this subnetwork has 205 nodes and is enriched in co-regulators and other tfs that physically interact with the 18 tfs ( and ). we further linked protein kinases that are likely […]

PMCID: 3332054
PMID: 22253195
DOI: 10.1002/humu.22026

[…] the table reports only kinases whose substrates were significantly enriched (p < 0.01)., subsequently, we focused on protein–protein interactions, using the gather [chang and nevins, ] and genes2networks [berger et al., ; see supp. methods] web-based tools. of note, the only protein displaying significant interactor enrichment in both ptpn11 and shoc2 signatures with both tools […]


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Genes2Networks institution(s)
Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY, USA

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