GenCLiP

[…] ere were 643 upregulated and 538 downregulated genes in SWOZ2-BCNU cells. The volcano plots of differentially expressed genes are shown in Fig. . These differentially expressed genes were analysed by GenCliP 2.0 software to annotate gene functions. Sorting by the negative value of the log (p-value) of GO analysis is shown in Fig. . The top-ranking terms were related to apoptosis and programmed cel […]

[…] ndicate that the DE-miRNAs and DEGs described above may act in concert to participate in IPF. A total of 15 DE-miRNAs and 11 DEGs involved in this microRNA-target relationship have been identified by GenCLip 2.0 to be associated with cell differentiation, signal transduction, mesenchymal stem cells, extracellular matrix, cell migration, and apoptosis. At the same time, we analyzed the 67 DEGs in o […]

[…] ug resistant ability enhancing. Perhaps this explains in part why the lower remission and higher recurrent were happened to patients with metastasis after chemotherapy treatment.Analysis results from GenCLiP 2.0 suggested that WNT pathway was involved in aberrant signaling pathways between metastatic and primary CRC, as well as between SW480 and SW620 cells. The main oncoprotein in colorectal canc […]

[…] es. Thirdly, the functions and annotations of the genes were searched in Ensembl and NCBI, if no available description or gene information were identified, the biomedical literature was searched with GenCLiP 2.0 (). When multiple biomedical functions were listed, functions related to gastrointestinal activity were prioritized for annotation. Fourthly, for a subset of genes Unigene (), Genevestigat […]

[…] rentially expressed genes between young and older breast cancer tissues. Delta was set to 0.6, and the threshold of FDR was set to 0.182. The differentially expressed genes were further analyzed with GenCLiP on-line software [, ] (http://ci.smu.edu.cn) to annotate gene functions and perform KEGG Pathway analysis. […]

[…] Other tools that enable literature-based knowledge discovery include GenCLiP () and FAUN (). GenCLiP is a Windows application that offers clustering of genes and terms based on the literature. It also generates gene networks based on co-occurrence of genes in the liter […]