Genes2Networks

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]