MetaCore from Thomson Reuters was used to perform data mining and pathway analysis for the differentially regulated microRNAs and genes.
To build the gene network from the differentially regulated genes, we used MetaCore (Thomson routers) data mining and pathway analysis database.
For the remaining four examples, i.e., HL60, iHEP, iCM, and iPSc, GRNs were reconstructed from literature using text mining and pathway database tools.
Through literature mining and pathway analysis using different databases such as Gene Ontology (GO), and the Kyoto Encyclopedia of Gene and Genomics (KEGG), genes involved in immune/inflammatory responses were significantly enriched in up-regulated genes at different stages of PAD(p < 0.05), revealing a significant correlation between immune/inflammatory responses and disease progression.
Results from informatics approaches, including GO analysis, text-mining, and pathway analysis, also suggested that many of the candidate exons were related to neural events.
Text-mining and pathway analysis were performed for the DAS genes using MedScan® text-mining technology in PathwayStudio® (Ariadne Genomics) [28].
One the other hand, from a biotechnological point of view, the organism can be used for genome mining approaches and pathway engineering towards medically relevant rhizoxin derivatives.
Gene ontology mining and Ingenuity pathway analysis (IPA) also showed downregulation of genes involved in cell-cycle regulation (see Table 1 and Additional files 6 and 9A), further confirming that epithelial cells stay quiescent when co-cultured with mesenchymal cells.
Furthermore, identified six genes (TSPYL5, CD55, CCNE2, DCK, BBC3, and MUC1) susceptible to breast cancer were verified through the literature mining, GO analysis, and pathway functional enrichment analysis.
Six identified genes (TSPYL5, CD55, CCNE2, DCK, BBC3, and MUC1) susceptible to breast cancer were verified through the literature mining, GO analysis, and pathway functional enrichment analysis.
Interestingly, based on the hypothesis that antisense transcription is the norm rather than the exception, we included in the array design 1143 sequences artificially created as antisense to those derived by literature and pathway mining.
