Screening of genes related to lung cancer caused by smoking with RNA-Seq.
OBJECTIVE
To study the lung cancer caused by smoking from RNA-seq data and its mechanism at molecular level.


METHODS
We downloaded gene expression profile SRA (Sequence Read Archive) data from Gene Expression Omnibus database that included two samples: one was lung cancer tissue samples from smoker (GSM718710) and the other was from non-smoker (GSM718709). We analyzed differential expression of genes with packages software TopHat and Cufflinks, and did Gene Ontology (GO) function clustering of the differentially expressed genes by BLASTX. Then we utilized KEGG Orthology Based Annotation System (KOBAS) to make pathway annotation and do enrichment analysis of KEGG pathway. After that, we searched for probable alternative splicing of the selected differentially expressed genes and found closely-linked genes.


RESULTS
we screened 1603 differentially expressed genes, most of which were involved in cellular processes. We also identified that the possible alternative splicing of gene FCGBP might have an important impact on lung cancer.


CONCLUSIONS
These findings in this study may help better understand the relationship between smoking and lung cancer pathogenesis.
Department of Respiratory Medicine, Zhou Pu Hospital, Shanghai, China. chaozhouz@hotmail.com.
C
C
Zhou
H
H
Chen
L
L
Han
F
F
Xue
A
A
Wang
Y-J
YJ
Liang
D017398:Alternative Splicing; D015815:Cell Adhesion Molecules / Q000235:genetics*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008168:Lung / Q000378:metabolism*; D008175:Lung Neoplasms / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012907:Smoking / Q000235:genetics*
D015815:Cell Adhesion Molecules; C106607:FCGBP protein, human