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| Wang,Q.; Shi,C.-J.; Lv,S.-H.. |
| Different pathways act synergistically to participate in many biological processes. Thus, the purpose of our study was to extract dysregulated pathways to investigate the pathogenesis of colorectal cancer (CRC) based on the functional dependency among pathways. Protein-protein interaction (PPI) information and pathway data were retrieved from STRING and Reactome databases, respectively. After genes were aligned to the pathways, each pathway activity was calculated using the principal component analysis (PCA) method, and the seed pathway was discovered. Subsequently, we constructed the pathway interaction network (PIN), where each node represented a biological pathway based on gene expression profile, PPI data, as well as pathways. Dysregulated pathways... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Pathway interaction network; Colorectal cancer; Dysregulated pathways; Principal component analysis; Protein-protein interaction. |
| Ano: 2017 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2017000500602 |
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| Jiang,T.; Jiang,C.-Y.; Shu,J.-H.; Xu,Y.-J.. |
| The molecular mechanism of nasopharyngeal carcinoma (NPC) is poorly understood and effective therapeutic approaches are needed. This research aimed to excavate the attractor modules involved in the progression of NPC and provide further understanding of the underlying mechanism of NPC. Based on the gene expression data of NPC, two specific protein-protein interaction networks for NPC and control conditions were re-weighted using Pearson correlation coefficient. Then, a systematic tracking of candidate modules was conducted on the re-weighted networks via cliques algorithm, and a total of 19 and 38 modules were separately identified from NPC and control networks, respectively. Among them, 8 pairs of modules with similar gene composition were selected, and 2... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Nasopharyngeal carcinoma; Protein-protein interaction; Attract; Module; Cell division. |
| Ano: 2017 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2017000800602 |
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| Chen,Kai; Wu,Dajiang; Zhu,Xiaodong; Ni,Haijian; Wei,Xianzhao; Mao,Ningfang; Xie,Yang; Niu,Yunfei; Li,Ming. |
| In this study, we used microarray analysis to investigate the biogenesis and progression of intervertebral disc degeneration. The gene expression profiles of 37 disc tissue samples obtained from patients with herniated discs and degenerative disc disease collected by the National Cancer Institute Cooperative Tissue Network were analyzed. Differentially expressed genes between more and less degenerated discs were identified by significant analysis of microarray. A total of 555 genes were significantly overexpressed in more degenerated discs with a false discovery rate of < 3%. Functional annotation showed that these genes were significantly associated with membrane-bound vesicles, calcium ion binding and extracellular matrix. Protein-protein interaction... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Genes; Intervertebral disc degeneration; Molecular classification; Protein-protein interaction. |
| Ano: 2013 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572013000300021 |
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| Xu,H.; Ma,J.; Wu,J.; Chen,L.; Sun,F.; Qu,C.; Zheng,D.; Xu,S.. |
| The present study screened potential genes related to lung adenocarcinoma, with the aim of further understanding disease pathogenesis. The GSE2514 dataset including 20 lung adenocarcinoma and 19 adjacent normal tissue samples from 10 patients with lung adenocarcinoma aged 45-73 years was downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) between the two groups were screened using the t-test. Potential gene functions were predicted using functional and pathway enrichment analysis, and protein-protein interaction (PPI) networks obtained from the STRING database were constructed with Cytoscape. Module analysis of PPI networks was performed through MCODE in Cytoscape. In total, 535 upregulated and 465 downregulated DEGs were... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Lung adenocarcinoma; Pathogenesis; Differentially expressed genes; Protein-protein interaction; Network module. |
| Ano: 2016 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2016000300601 |
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