GenCLiP

[…] were built with the aid of cytoscape [], using the central nodes identified in each comparison. semantic relationships were identified between genes and keywords with the text mining tool genclip []. we searched for relationships using the keywords “immune response”, “t regulatory cells”, “autophagy”, “ubiquitin-proteasome”, “endocytosis”, “fibrosis”, “inflammation”, “extracellular […]

[…] were built with the aid of cytoscape [], using the central nodes identified in each comparison. semantic relationships were identified between genes and keywords with the text mining tool genclip []. we searched for relationships using the keywords “immune response”, “t regulatory cells”, “autophagy”, “ubiquitin-proteasome”, “endocytosis”, “fibrosis”, “inflammation”, “extracellular […]

[…] analysis results of ppis were downloaded from string, and modified by cytoscape (http://www.cytoscape.org/). according to the analysis of string, nodes with higher degree in the ppi were put into genclip 2.0 (http://ci.smu.edu.cn/genclip2.0/confirm_keywords.php), which is an online tool for literature mining of genes. genclip could generate keywords of genes in previous literatures to help us […]

[…] 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 […]

[…] subsequent to analysis of the modules, the degs in the modules were analyzed using literature mining to explore their relevance in previous studies. the gene cluster with literature profiles 2.0 (genclip 2.0; http://ci.smu.edu.cn/) () online tool was used for literature mining of human genes and network. the input gene set was the key gene set in the ppi network. the literature mining gene […]

[…] interaction were considered as hub nodes., the association among nodes with a higher degree of interaction in the network and the associated biological functions were analyzed by literature mining. genclip 2.0 () (http://ci.smu.edu.cn/genclip2.0/confirm_keywords.php) is an online tool used for the literature mining analysis of human genes and networks. hub gene sets obtained from the ppi […]

[…] elucidate the correlations between mirnas and potential target genes, mirna-gene network analyses were generated by cytoscape (). text mining of the 17 de-mirnas and 17 degs was performed using the genclip 2.0 software. the occurrence frequency of terms in corresponding gene-related literature including cell differentiation, signal transduction, mesenchymal stem cells, transforming growth […]