Page 6 - B.Bioinformatics and systems biology

[B. Bioinformatics and systems biology-5]

A bioinformatic approach to the identification of genetic

markers of Idiopathic pulmonary fibrosis (IPF)

Sungmin Park¹, Seungmin Song¹, Junghyun Jung², Jong Wha Joanne Joo¹˙*

¹Computer Science and Engineering, Dongguk University, Seoul 04620, Republic of Korea, ²Life Science, Dongguk

University, Seoul 04620, Republic of Korea

Idiopathic pulmonary fibrosis (IPF) is one of the chronic and fatal interstitial lung diseases. RNA sequencing and
microarray experiments enables the determination of genes whose expression levels are significantly different in IPF

disease group compared with healthy control group. Two human lung transcriptomic data sets were obtained from

EBI-ArrayExpress, and their profiles were RNA-Seq data GSE52463 (8 IPF, 7 controls) and microarray experiments
GSE38958 (17 IPF, 6 controls). Total 661 genes were identified as differentially expressed genes (DEGs) in both two
data sets (P-value < 0.05) via oligo, limma, and DESeq R packages. Among total DEGs, 317 genes were significantly

up-regulated genes and 341 genes were down-regulated genes. In order to confirm the systemic functions of the
obtained DEGs, we performed gene set enrichment analysis and functional annotation by Database for Annotation,

Visualization and Integrated Discovery. Additionally, protein-protein networks using DEGs were established through
search tool for the retrieval of Interacting Genes/Proteins and finally visualized using Cytoscape. We found several

genes which showed significant correlations with IPF. The resulted genes can be suggested as potential genetic
markers or specific druggable target for IPF.