Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer
TU Dortmund Univ, Fac Stat, Dortmund, Germany..
Dortmund Univ, Leibniz Res Ctr Working Environm & Human Factors, Dortmund, Germany..
TU Dortmund Univ, Fac Stat, Dortmund, Germany..
TU Dortmund Univ, Fac Stat, Dortmund, Germany..
Show others and affiliations
2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 11, article id e0187246Article in journal (Refereed) Published
Abstract [en]

Non-small cell lung cancer (NSCLC) represents a genomically unstable cancer type with extensive copy number aberrations. The relationship of gene copy number alterations and subsequent mRNA levels has only fragmentarily been described. The aim of this study was to conduct a genome-wide analysis of gene copy number gains and corresponding gene expression levels in a clinically well annotated NSCLC patient cohort (n = 190) and their association with survival. While more than half of all analyzed gene copy number-gene expression pairs showed statistically significant correlations (10,296 of 18,756 genes), high correlations, with a correlation coefficient >0.7, were obtained only in a subset of 301 genes (1.6%), including KRAS, EGFR and MDM2. Higher correlation coefficients were associated with higher copy number and expression levels. Strong correlations were frequently based on few tumors with high copy number gains and correspondingly increased mRNA expression. Among the highly correlating genes, GO groups associated with posttranslational protein modifications were particularly frequent, including ubiquitination and neddylation. In a meta-analysis including 1,779 patients we found that survival associated genes were overrepresented among highly correlating genes (61 of the 301 highly correlating genes, FDR adjusted p<0.05). Among them are the chaperone CCT2, the core complex protein NUP107 and the ubiquitination and neddylation associated protein CAND1. In conclusion, in a comprehensive analysis we described a distinct set of highly correlating genes. These genes were found to be overrepresented among survival-associated genes based on gene expression in a large collection of publicly available datasets.

Place, publisher, year, edition, pages
2017. Vol. 12, no 11, article id e0187246
National Category
Cancer and Oncology
Identifiers
URN: urn:nbn:se:uu:diva-341934DOI: 10.1371/journal.pone.0187246ISI: 000414572100012PubMedID: 29112949OAI: oai:DiVA.org:uu-341934DiVA, id: diva2:1183394
Available from: 2018-02-16 Created: 2018-02-16 Last updated: 2018-11-16Bibliographically approved

Open Access in DiVA

fulltext(5808 kB)19 downloads
File information
File name FULLTEXT01.pdfFile size 5808 kBChecksum SHA-512
2f0c92677c5929b1328f178bdbc2ab1a5da4a3fa84dd86bf60dcdff8dd282ebd5c26ff91110534ef92061b142220d9e4d1ed5e6ce103edb2444e1d09d9bdf608
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Holmberg, LarsBotling, JohanMicke, Patrick
By organisation
Endocrine SurgeryClinical and experimental pathology
In the same journal
PLoS ONE
Cancer and Oncology

Search outside of DiVA

GoogleGoogle Scholar
Total: 19 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 30 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf