PMID- 32024523
OWN - NLM
STAT- MEDLINE
DCOM- 20201216
LR  - 20231103
IS  - 1755-8794 (Electronic)
IS  - 1755-8794 (Linking)
VI  - 13
IP  - 1
DP  - 2020 Feb 5
TI  - The cox-filter method identifies respective subtype-specific lncRNA prognostic 
      signatures for two human cancers.
PG  - 18
LID - 10.1186/s12920-020-0691-4 [doi]
LID - 18
AB  - BACKGROUND: The most common histological subtypes of esophageal cancer are 
      squamous cell carcinoma (ESCC) and adenocarcinoma (EAC). It has been demonstrated 
      that non-marginal differences in gene expression and somatic alternation exist 
      between these two subtypes; consequently, biomarkers that have prognostic values 
      for them are expected to be distinct. In contrast, laryngeal squamous cell cancer 
      (LSCC) has a better prognosis than hypopharyngeal squamous cell carcinoma (HSCC). 
      Likewise, subtype-specific prognostic signatures may exist for LSCC and HSCC. 
      Long non-coding RNAs (lncRNAs) hold promise for identifying prognostic signatures 
      for a variety of cancers including esophageal cancer and head and neck squamous 
      cell carcinoma (HNSCC). METHODS: In this study, we applied a novel feature 
      selection method capable of identifying specific prognostic signatures uniquely 
      for each subtype - the Cox-filter method - to The Cancer Genome Atlas esophageal 
      cancer and HSNCC RNA-Seq data, with the objectives of constructing 
      subtype-specific prognostic lncRNA expression signatures for esophageal cancer 
      and HNSCC. RESULTS: By incorporating biological relevancy information, the lncRNA 
      lists identified by the Cox-filter method were further refined. The resulting 
      signatures include genes that are highly related to cancer, such as H19 and 
      NEAT1, which possess perfect prognostic values for esophageal cancer and HNSCC, 
      respectively. CONCLUSIONS: The Cox-filter method is indeed a handy tool to 
      identify subtype-specific prognostic lncRNA signatures. We anticipate the method 
      will gain wider applications.
FAU - Tian, Suyan
AU  - Tian S
AUID- ORCID: 0000-0002-5942-1542
AD  - Division of Clinical Research, The First Hospital of Jilin University, 1Xinmin 
      Street, Changchun, Jilin, 130021, People's Republic of China. 
      windytian@hotmail.com.
FAU - Wang, Chi
AU  - Wang C
AD  - Department of Biostatistics, College of Public Health, University of Kentucky, 
      800 Rose St, Lexington, KY, 40536, USA.
AD  - Markey Cancer Center, University of Kentucky, 800 Rose St, Lexington, KY, 40536, 
      USA.
FAU - Zhang, Jing
AU  - Zhang J
AD  - School of Life Science, 2699 Qianjin Street, Changchun, Jilin, 130012, People's 
      Republic of China.
FAU - Yu, Dan
AU  - Yu D
AD  - Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin 
      University, 218 Ziqiang Road, Changchun, Jilin, 130041, People's Republic of 
      China. yudan19792003@163.com.
LA  - eng
GR  - P30 CA177558/CA/NCI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20200205
PL  - England
TA  - BMC Med Genomics
JT  - BMC medical genomics
JID - 101319628
RN  - 0 (RNA, Long Noncoding)
RN  - 0 (RNA, Neoplasm)
SB  - IM
MH  - *Carcinoma, Squamous Cell/genetics/metabolism/mortality
MH  - *Databases, Genetic
MH  - Disease-Free Survival
MH  - *Esophageal Neoplasms/genetics/metabolism/mortality
MH  - Gene Expression Profiling
MH  - *Gene Expression Regulation, Neoplastic
MH  - *Head and Neck Neoplasms/genetics/metabolism/mortality
MH  - Humans
MH  - Kaplan-Meier Estimate
MH  - *RNA, Long Noncoding/genetics/metabolism
MH  - *RNA, Neoplasm/genetics/metabolism
MH  - *Squamous Cell Carcinoma of Head and Neck/genetics/metabolism/mortality
MH  - Survival Rate
PMC - PMC7003323
OTO - NOTNLM
OT  - Cox regression model
OT  - Esophageal cancer
OT  - Head and neck squamous cell carcinoma (HNSCC)
OT  - Long non-coding RNA (lncRNA)
OT  - Prognostic signature
COIS- The authors declare that they have no competing interests.
EDAT- 2020/02/07 06:00
MHDA- 2020/12/17 06:00
PMCR- 2020/02/05
CRDT- 2020/02/07 06:00
PHST- 2019/09/16 00:00 [received]
PHST- 2020/01/29 00:00 [accepted]
PHST- 2020/02/07 06:00 [entrez]
PHST- 2020/02/07 06:00 [pubmed]
PHST- 2020/12/17 06:00 [medline]
PHST- 2020/02/05 00:00 [pmc-release]
AID - 10.1186/s12920-020-0691-4 [pii]
AID - 691 [pii]
AID - 10.1186/s12920-020-0691-4 [doi]
PST - epublish
SO  - BMC Med Genomics. 2020 Feb 5;13(1):18. doi: 10.1186/s12920-020-0691-4.