PMID- 31850075
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20201001
IS  - 1664-8021 (Print)
IS  - 1664-8021 (Electronic)
IS  - 1664-8021 (Linking)
VI  - 10
DP  - 2019
TI  - Identification of Common and Subtype-Specific Mutated Sub-Pathways for a Cancer.
PG  - 1228
LID - 10.3389/fgene.2019.01228 [doi]
LID - 1228
AB  - The heterogeneity of cancer is a big obstacle for cancer diagnosis and treatment. 
      Prioritizing combinations of driver genes that mutate in most patients of a 
      specific cancer or a subtype of this cancer is a promising way to tackle this 
      problem. Here, we developed an empirical algorithm, named PathMG, to identify 
      common and subtype-specific mutated sub-pathways for a cancer. By analyzing 
      mutation data of 408 samples (Lung-data1) for lung cancer, three sub-pathways 
      each covering at least 90% of samples were identified as the common sub-pathways 
      of lung cancer. These sub-pathways were enriched with mutated cancer genes and 
      drug targets and were validated in two independent datasets (Lung-data2 and 
      Lung-data3). Especially, applying PathMG to analyze two major subtypes of lung 
      cancer, lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LSCC), we 
      identified 13 subtype-specific sub-pathways with at least 0.25 mutation frequency 
      difference between LUAD and LSCC samples in Lung-data1, and 12 of the 13 
      sub-pathways were reproducible in Lung-data2 and Lung-data3. Similar analyses 
      were done for colorectal cancer. Together, PathMG provides us a novel tool to 
      identify potential common and subtype-specific sub-pathways for a cancer, which 
      can provide candidates for cancer diagnoses and sub-pathway targeted treatments.
CI  - Copyright (c) 2019 Yan, Deng, Chen, Cheng, He, Guan, Li, Xie, Xia, Gu and Guo.
FAU - Yan, Haidan
AU  - Yan H
AD  - Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department 
      of Bioinformatics, The School of Basic Medical Sciences, Fujian Medical 
      University, Fuzhou, China.
AD  - Key Laboratory of Medical Bioinformatics, Fujian Medical University, Fuzhou, 
      China.
FAU - Deng, Xusheng
AU  - Deng X
AD  - Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department 
      of Bioinformatics, The School of Basic Medical Sciences, Fujian Medical 
      University, Fuzhou, China.
AD  - Key Laboratory of Medical Bioinformatics, Fujian Medical University, Fuzhou, 
      China.
FAU - Chen, Haifeng
AU  - Chen H
AD  - Department of General Surgery, Fuzhou Second Hospital Affiliated to Xiamen 
      University, Xiamen, China.
FAU - Cheng, Jun
AU  - Cheng J
AD  - Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department 
      of Bioinformatics, The School of Basic Medical Sciences, Fujian Medical 
      University, Fuzhou, China.
AD  - Key Laboratory of Medical Bioinformatics, Fujian Medical University, Fuzhou, 
      China.
FAU - He, Jun
AU  - He J
AD  - Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department 
      of Bioinformatics, The School of Basic Medical Sciences, Fujian Medical 
      University, Fuzhou, China.
AD  - Key Laboratory of Medical Bioinformatics, Fujian Medical University, Fuzhou, 
      China.
FAU - Guan, Qingzhou
AU  - Guan Q
AD  - Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department 
      of Bioinformatics, The School of Basic Medical Sciences, Fujian Medical 
      University, Fuzhou, China.
AD  - Key Laboratory of Medical Bioinformatics, Fujian Medical University, Fuzhou, 
      China.
FAU - Li, Meifeng
AU  - Li M
AD  - Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department 
      of Bioinformatics, The School of Basic Medical Sciences, Fujian Medical 
      University, Fuzhou, China.
AD  - Key Laboratory of Medical Bioinformatics, Fujian Medical University, Fuzhou, 
      China.
FAU - Xie, Jiajing
AU  - Xie J
AD  - Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department 
      of Bioinformatics, The School of Basic Medical Sciences, Fujian Medical 
      University, Fuzhou, China.
AD  - Key Laboratory of Medical Bioinformatics, Fujian Medical University, Fuzhou, 
      China.
FAU - Xia, Jie
AU  - Xia J
AD  - Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department 
      of Bioinformatics, The School of Basic Medical Sciences, Fujian Medical 
      University, Fuzhou, China.
AD  - Key Laboratory of Medical Bioinformatics, Fujian Medical University, Fuzhou, 
      China.
FAU - Gu, Yunyan
AU  - Gu Y
AD  - Department of Systems Biology, College of Bioinformatics Science and Technology, 
      Harbin Medical University, Harbin, China.
FAU - Guo, Zheng
AU  - Guo Z
AD  - Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department 
      of Bioinformatics, The School of Basic Medical Sciences, Fujian Medical 
      University, Fuzhou, China.
AD  - Key Laboratory of Medical Bioinformatics, Fujian Medical University, Fuzhou, 
      China.
LA  - eng
PT  - Journal Article
DEP - 20191128
PL  - Switzerland
TA  - Front Genet
JT  - Frontiers in genetics
JID - 101560621
PMC - PMC6892778
OTO - NOTNLM
OT  - cancer genes
OT  - common sub-pathways
OT  - drug targets
OT  - mutation
OT  - subtype-specific sub-pathways
EDAT- 2019/12/19 06:00
MHDA- 2019/12/19 06:01
PMCR- 2019/11/28
CRDT- 2019/12/19 06:00
PHST- 2019/09/04 00:00 [received]
PHST- 2019/11/06 00:00 [accepted]
PHST- 2019/12/19 06:00 [entrez]
PHST- 2019/12/19 06:00 [pubmed]
PHST- 2019/12/19 06:01 [medline]
PHST- 2019/11/28 00:00 [pmc-release]
AID - 10.3389/fgene.2019.01228 [doi]
PST - epublish
SO  - Front Genet. 2019 Nov 28;10:1228. doi: 10.3389/fgene.2019.01228. eCollection 
      2019.