Lists2Networks

[…] inhibitor sp600125 [-]. using david, we collected the lists of official symbols of regulated genes in those studies, as well as of the egf-regulated genes from this study and submitted them to the lists2networks analysis program []. the program compares lists for mutual overlaps within specific categories, e.g., targets of protein kinases, ontological biological process or omim disease gene […]

[…] n=79) were obtained from the amigo 2 database (http://amigo.geneontology.org/amigo). ppi gene network images were generated using genemania () based on ppi interactions from databases utilized by lists2networks (; )., comparisons with known imprinted genes were conducted using lists compiled from rat, mouse, and human (www.geneimprint.com), considering gene ids and aliases with status listed […]

[…] and merging different platforms, dealing with empty cells and negative numbers, selecting data subsets and differentially expressed genes using rankprod, gene lists annotation using the lists2networks algorithm, clustering and comparing lists and promoter analysis . the workflow diagram describing meta-profiling and cluster analysis is shown in briefly, for the data deposited […]

[…] the following databases and publications: biogrid , hprd , innatedb , intact , kegg , kea , mint , mips , dip , bind , biocarta, pdzbase and ppid –. for the pathway enrichment analysis we used lists2networks to compute enrichment for biocarta pathways, gene ontology , wikipathways , as well as several other gene set libraries we developed ., community structure within the nmmhciia ppi […]

[…] filtered out, and the semantic similarities of gene classes were calculated using the gosemsim software package. the gene class with the highest functional consistency was selected, and then the lists2networks web-based system was used to analyse regulatory relationships between mirnas and gene classes. the functional enrichment of the gene classes was assessed based on gene ontology (go) […]

[…] 1 (il-1), retinoic acid (ra), ephrin as and sp600125, a specific inhibitor of jnk [-]. the numbers of genes present in each list analyzed are given in additional file : table s5. we used the lists2networks program for comparisons and collected both the matrix of p-values for overlapping of related lists, as well as bonferoni-corrected lists of gene ontology categories ‘biological […]