GRNInfer

[…] regression; cs: control strength; em: expectation-maximization; elu: elutriation; go: gene ontology; tf: transcription factor; tfa: transcription factor activity; nca: network component analysis; grninfer: gene regulatory network inference; rrna: ribosomal rna; utr: untranslated region; rnp: nucleolar ribonucleoprotein; rbps: rna binding proteins; rpm: random periods model., the authors […]

[…] algorithm. the top 50 genes, including irs1/2, were used as target genes to determine the gene regulatory networks and next the sub-networks of irs1 and irs2 in hcv-huh7 and huh7 cells using gene regulatory network inference tool, an algorithm based on linear programming and the decomposition process. the irs1/2 sub-networks were divided into upstream/downstream groups […]

[…] 48 different pearson mutual-positive-correlation epidermal growth factor receptor (egfr_1)-activatory molecular feedback, up- and down-stream network was constructed from 171 overlapping of 366 grninfer and 223 pearson under egfr_1 cc ≥0.25 in high lung adenocarcinoma compared with low human normal adjacent tissues. our identified egfr_1 inside-out upstream activated molecular network […]

[…] compared with lower human normal adjacent tissues from the corresponding comp-stimulated (≥0.25) or inhibited (pearson cc≤−0.25) overlapping molecules of pearson correlation coefficient (cc) and grninfer, respectively. comp complete different activated and inhibited (all no positive correlation, pearson cc< 0.25) mechanisms networks of higher lung adenocarcinoma and lower human normal […]

[…] with high expression (fold change ≥2) were identified and computed., amely-activated upstream regulation molecular networks in non-tumor hepatitis/cirrhotic tissues and hcc were constructed by grninfer () and published studies (–), and illustrated by gvedit tool, respectively., the biological processes of amely-activated upstream regulation networks in non-tumor hepatitis/cirrhotic tissues […]

[…] go terms from the same activated pthlh go-molecular network of hcc compared with the corresponding activated go-molecular network of no-tumor hepatitis/cirrhotic tissues, and constructed network by grninfer [] and our articles [–] and illustrated by gvedit tool., biological processes and occurrence numbers of the same activated high expression (fold change ≥2) pthlh feedback-mediated cell […]