PMID- 27273946
OWN - NLM
STAT- MEDLINE
DCOM- 20160701
LR  - 20160609
IS  - 1107-0625 (Print)
IS  - 1107-0625 (Linking)
VI  - 21
IP  - 2
DP  - 2016 Mar-Apr
TI  - Identification of disrupted pathways in ulcerative colitis-related colorectal 
      carcinoma by systematic tracking the dysregulated modules.
PG  - 366-74
AB  - PURPOSE: The aim of this study was to identify the altered biological pathways 
      associated with ulcerative colitis (UC)-related colorectal carcinoma (CRC) by 
      systematic tracking the dysregulated modules from re-weighted protein- protein 
      interaction (PPI) networks based on the expression profiles from normal, UC and 
      various stages of CRC. METHODS: We firstly recruited the UC- and CRC-related 
      microarray data from ArrayExpress database, and obtained 8 expression profiles 
      which contained 5 conditions (normal, UC, early stage CRC, stage II CRC and stage 
      III CRC). Then, the PPI networks of normal and different disease stages were 
      constructed and re-weighted using Pearson correlation coefficient (PCC). Next, 
      the condition-specific modules were extracted from 5 PPI networks via 
      clique-merging algorithm, and altered modules were captured on the basis of 
      module correlation density (MCD). Subsequently, the gene compositions of altered 
      modules and gene differential expressions in different disease stages were 
      identified to screen the dysregulated genes. Finally, pathways enrichment 
      analyses for the genes in altered modules and differentially expressed genes 
      (DEGs) were implemented. RESULTS: The extensive changes of gene correlations 
      existed in 5 condition-specific PPI networks, which made different MCDs among 
      different disease stages. The same number of modules (N=1952) were explored in 5 
      PPI networks. By comparing with normal condition, there were 463, 791, 1060 and 
      345 altered modules in UC, early stage CRC, stage II and III CRC, respectively. 
      Overall, 77, 110, 170 and 110 common genes were identified between genes of 
      altered modules and DEGs in UC, early stage CRC, stage II CRC and stage III CRC, 
      respectively. Functional enrichment analyses indicated that cell cycle and oocyte 
      meiosis were the common and most significant pathways in colonic diseases. 
      CONCLUSIONS: Tracking the altered modules from PPI networks is useful to uncover 
      disrupted pathways in colonic diseases. Cell cycle and oocyte meiosis might be 
      associated with the pathophysiological background of colonic diseases.
FAU - Wu, Deshun
AU  - Wu D
AD  - Department of General Surgery, The Seventh People's Hospital of Ji-nan, Ji-nan 
      251400, Shandong Province, China.
FAU - Li, Qing
AU  - Li Q
FAU - Song, Guixiang
AU  - Song G
FAU - Lu, Jun
AU  - Lu J
LA  - eng
PT  - Journal Article
PL  - Cyprus
TA  - J BUON
JT  - Journal of B.U.ON. : official journal of the Balkan Union of Oncology
JID - 100883428
RN  - 0 (Biomarkers, Tumor)
SB  - IM
MH  - Adenoma/etiology/*genetics/metabolism/pathology
MH  - Biomarkers, Tumor/*genetics/metabolism
MH  - Carcinoma/etiology/*genetics/metabolism/pathology
MH  - Case-Control Studies
MH  - Cell Transformation, Neoplastic/*genetics/metabolism/pathology
MH  - Colitis, Ulcerative/complications/diagnosis/*genetics/metabolism
MH  - Colorectal Neoplasms/etiology/*genetics/metabolism/pathology
MH  - Databases, Genetic
MH  - Disease Progression
MH  - Gene Expression Profiling/methods
MH  - Gene Expression Regulation, Neoplastic
MH  - Gene Regulatory Networks
MH  - Humans
MH  - Neoplasm Staging
MH  - Oligonucleotide Array Sequence Analysis
MH  - Protein Interaction Mapping
MH  - Protein Interaction Maps
MH  - Signal Transduction
EDAT- 2016/06/09 06:00
MHDA- 2016/07/02 06:00
CRDT- 2016/06/09 06:00
PHST- 2016/06/09 06:00 [entrez]
PHST- 2016/06/09 06:00 [pubmed]
PHST- 2016/07/02 06:00 [medline]
PST - ppublish
SO  - J BUON. 2016 Mar-Apr;21(2):366-74.