PMID- 24476546
OWN - NLM
STAT- MEDLINE
DCOM- 20150608
LR  - 20140729
IS  - 1943-3670 (Electronic)
IS  - 0022-3492 (Linking)
VI  - 85
IP  - 8
DP  - 2014 Aug
TI  - Prioritization of candidate genes for periodontitis using multiple computational 
      tools.
PG  - 1059-69
LID - 10.1902/jop.2014.130523 [doi]
AB  - BACKGROUND: Both genetic and environmental factors contribute to the development 
      of periodontitis. Genetic studies identified a variety of candidate genes for 
      periodontitis. The aim of the present study is to identify the most promising 
      candidate genes for periodontitis using an integrative gene ranking method. 
      METHODS: Seed genes that were confirmed to be associated with periodontitis were 
      identified using text mining. Three types of candidate genes were then extracted 
      from different resources (expression profiles, genome-wide association studies). 
      Combining the seed genes, four freely available bioinformatics tools (ToppGene, 
      DIR, Endeavour, and GPEC) were integrated for prioritization of candidate genes. 
      Candidate genes that identified with at least three programs and ranked in the 
      top 20 by each program were considered the most promising. RESULTS: 
      Prioritization analysis resulted in 21 promising genes involved or potentially 
      involved in periodontitis. Among them, IL18 (interleukin 18), CD44 (CD44 
      molecule), CXCL1 (chemokine [CXC motif] ligand 1), IL6ST (interleukin 6 signal 
      transducer), MMP3 (matrix metallopeptidase 3), MMP7, CCR1 (chemokine [C-C motif] 
      receptor 1), MMP13, and TLR9 (Toll-like receptor 9) had been associated with 
      periodontitis. However, the roles of other genes, such as CSF3 (colony 
      stimulating factor 3 receptor), CD40, TNFSF14 (tumor necrosis factor receptor 
      superfamily, member 14), IFNB1 (interferon-beta1), TIRAP (toll-interleukin 1 
      receptor domain containing adaptor protein), IL2RA (interleukin 2 receptor alpha), 
      ETS1 (v-ets avian erythroblastosis virus E26 oncogene homolog 1), GADD45B (growth 
      arrest and DNA-damage-inducible 45 beta), BIRC3 (baculoviral IAP repeat containing 
      3), VAV1 (vav 1 guanine nucleotide exchange factor), COL5A1 (collagen, type V, 
      alpha1), and C3 (complement component 3), have not been investigated thoroughly in 
      the process of periodontitis. These genes are mainly involved in bacterial 
      infection, immune response, and inflammatory reaction, suggesting that further 
      characterizing their roles in periodontitis will be important. CONCLUSIONS: A 
      combination of computational tools will be useful in mining candidate genes for 
      periodontitis. These theoretical results provide new clues for experimental 
      biologists to plan targeted experiments.
FAU - Zhan, Yuanbo
AU  - Zhan Y
AD  - Department of Periodontology and Oral Mucosa, Second Affiliated Hospital of 
      Harbin Medical University, Harbin, China.
FAU - Zhang, Ruimin
AU  - Zhang R
FAU - Lv, Hongchao
AU  - Lv H
FAU - Song, Xuejing
AU  - Song X
FAU - Xu, Xiaoman
AU  - Xu X
FAU - Chai, Lin
AU  - Chai L
FAU - Lv, Wenhua
AU  - Lv W
FAU - Shang, Zhenwei
AU  - Shang Z
FAU - Jiang, Yongshuai
AU  - Jiang Y
FAU - Zhang, Ruijie
AU  - Zhang R
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140130
PL  - United States
TA  - J Periodontol
JT  - Journal of periodontology
JID - 8000345
RN  - 0 (Cytokines)
RN  - 0 (Interleukins)
RN  - 0 (Tumor Necrosis Factors)
RN  - EC 3.4.24.- (Matrix Metalloproteinases)
SB  - IM
MH  - Computational Biology
MH  - Cytokines/genetics
MH  - Data Mining
MH  - Databases as Topic
MH  - Gene Expression Profiling
MH  - Genetic Association Studies/*methods
MH  - Humans
MH  - Interleukins/genetics
MH  - Matrix Metalloproteinases/genetics
MH  - Periodontitis/*genetics
MH  - Tumor Necrosis Factors/genetics
OTO - NOTNLM
OT  - Computational biology
OT  - genetic association studies
OT  - genomics
OT  - periodontitis.
EDAT- 2014/01/31 06:00
MHDA- 2015/06/09 06:00
CRDT- 2014/01/31 06:00
PHST- 2014/01/31 06:00 [entrez]
PHST- 2014/01/31 06:00 [pubmed]
PHST- 2015/06/09 06:00 [medline]
AID - 10.1902/jop.2014.130523 [doi]
PST - ppublish
SO  - J Periodontol. 2014 Aug;85(8):1059-69. doi: 10.1902/jop.2014.130523. Epub 2014 
      Jan 30.