ArticleComputational and mathematical methods in medicine2015
Temporal Identification of Dysregulated Genes and Pathways in Clear Cell Renal Cell Carcinoma Based on Systematic Tracking of Disrupted Modules.
Article in Computational and mathematical methods in medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Efficient extraction via titanium organic frameworks facilitates in-depth profiling of urinary exosome metabolite fingerprints.Analytical and bioanalytical chemistry · 2025Article
- Research on molecular characteristics of ADME-related genes in kidney renal clear cell carcinoma.Scientific reports · 2024Article
- The establishment of kidney cancer organoid line in drug testing.Cancer medicine · 2024Article
- High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes.Oncotarget · 2017Article
- First-in-Human Phase 1 Trial of Agarose Beads Containing Murine RENCA Cells in Advanced Solid Tumors.Cancer growth and metastasis · 2016Article
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Abstract
objectiveThe objective of this work is to identify dysregulated genes and pathways of ccRCC temporally according to systematic tracking of the dysregulated modules of reweighted Protein-Protein Interaction (PPI) networks.
methodsFirstly, normal and ccRCC PPI network were inferred and reweighted based on Pearson correlation coefficient (PCC). Then, we identified altered modules using maximum weight bipartite matching and ranked them in nonincreasing order. Finally, gene compositions of altered modules were analyzed, and pathways enrichment analyses of genes in altered modules were carried out based on Expression Analysis Systematic Explored (EASE) test.
resultsWe obtained 136, 576, 693, and 531 disrupted modules of ccRCC stages I, II, III, and IV, respectively. Gene composition analyses of altered modules revealed that there were 56 common genes (such as MAPK1, CCNA2, and GSTM3) existing in the four stages. Besides pathway enrichment analysis identified 5 common pathways (glutathione metabolism, cell cycle, alanine, aspartate, and glutamate metabolism, arginine and proline metabolism, and metabolism of xenobiotics by cytochrome P450) across stages I, II, III, and IV.
conclusionsWe successfully identified dysregulated genes and pathways of ccRCC in different stages, and these might be potential biological markers and processes for treatment and etiology mechanism in ccRCC.
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