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2015 ; 2015
(ä): 313740
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Temporal Identification of Dysregulated Genes and Pathways in Clear Cell Renal
Cell Carcinoma Based on Systematic Tracking of Disrupted Modules
#MMPMID26543493
Wang SM
; Sun ZQ
; Li HY
; Wang J
; Liu QY
Comput Math Methods Med
2015[]; 2015
(ä): 313740
PMID26543493
show ga
OBJECTIVE: The 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. METHODS:
Firstly, 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. RESULTS: We 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. CONCLUSIONS: We 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.