Tumor Biology

, Volume 36, Issue 3, pp 1849–1857 | Cite as

RETRACTED ARTICLE: A comprehensive analysis of candidate genes and pathways in pancreatic cancer

  • Jie Liu
  • Jun Li
  • Hali Li
  • Aidong Li
  • Biou Liu
  • Liou Han
Research Article

Abstract

The study aimed to dissect the molecular mechanism of pancreatic cancer by a range of bioinformatics approaches. Three microarray datasets (GSE32676, GSE21654, and GSE14245) were downloaded from Gene Expression Omnibus database. Differentially expressed genes (DEGs) with logarithm of fold change (|logFC|) >0.585 and p value <0.05 were identified between pancreatic cancer samples and normal controls. Transcription factors (TFs) were selected from the DEGs based on TRASFAC database. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed for the DEGs using The Database for Annotation, Visualization and Integrated Discovery (p value <0.05), followed by construction of protein-protein interaction (PPI) network using Search Tool for the Retrieval of Interacting Genes software. Latent pathway identification analysis was applied to analyze the DEGs-related pathways crosstalk and the pathways with high weight value were included in the pathway crosstalk network using Cytoscape. Sixty-five DEGs were screened out. CCAAT/enhancer-binding protein delta (CEBPD), FBJ osteosarcoma oncogene B (FOSB), Stratifin (SFN), Krüppel-like factor 5 (KLF5), Pentraxin 3 (PTX3), and nuclear receptor subfamily 4, group A, member 3 (NR4A3) were important TFs. Interleukin-6 (IL-6) was the hub node of the PPI network. DEGs were significantly enriched in NOD-like receptor signaling pathway which was primarily interacted with inflammation and immune related pathways (cytosolic DNA-sensing, hematopoietic cell lineage, intestinal immune network for IgA production and chemokine pathways). The study suggested CEBPD, FOSB, SFN, KLF5, PTX3, NR4A3, IL-6, and NOD-like receptor pathways were involved in pancreatic cancer.

Keywords

Pancreatic cancer Pathway crosstalk Protein-protein interaction Differentially expressed genes Gene ontology 

Abbreviations

TF

transcription factor

IL-6

interleukin-6

IL-1B

interleukin-1β

KRAS

V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog

TNF-α

tumor necrosis factor-alpha

EGF

epidermal growth factor

RMA

robust multiarray average

LogFC

logarithm of fold change

DAVID

The Database for Annotation, Visualization, and Integrated Discovery

GO

gene ontology

KEGG

Kyoto Encyclopedia of Genes and Genomes

BP

biological process

CC

cellular component

MF

molecular function

STRING

The Search Tool for the Retrieval of Interacting Genes

PPI

protein-protein interaction

LPIA

latent pathway identification analysis

DEGs

differentially expressed genes

IFN-γ

interferon-γ

SFN

stratifin

FOSB

FBJ osteosarcoma oncogene B

PTX3

pentraxin-related protein 3

NR4A3

nuclear receptor subfamily 4 group A, member 3

C/EBP delta

CCAAT/enhancer-binding protein delta

KLFs

Krüppel-like factors

NLRs

NOD-like receptors

MAPK

mitogen-activated protein kinase

Notes

Acknowledgments

This study was supported by Overseas Scholars Funds (grant no. 1054HQ081) and National Natural Science Foundation of China (grant no. 30340058).

Conflicts of interest

None

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Copyright information

© International Society of Oncology and BioMarkers (ISOBM) 2014

Authors and Affiliations

  • Jie Liu
    • 1
  • Jun Li
    • 1
  • Hali Li
    • 1
  • Aidong Li
    • 1
  • Biou Liu
    • 1
  • Liou Han
    • 1
  1. 1.Department of general surgeryThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina

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