Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues

View article
RT @mrbnack: #cantargia #CAN04 https://t.co/jQeStyU9aF
1614 days ago
RT @mrbnack: #cantargia #CAN04 https://t.co/jQeStyU9aF
1614 days ago
#cantargia #CAN04 https://t.co/jQeStyU9aF
Bioinformatics and Genomics

Main article text

 

Introduction

Materials and Methods

Selection of microarray datasets

Generation of gene expression matrix files and evaluation of data quality

Standard meta-analysis

External validation of the identified DEGs

Transcription factor binding site enrichment analysis

Finding prognostic genes for PDAC

Protein-protein interaction analysis

Gene ontology and pathway enrichment analysis of the DEGs

Results

Microarray datasets

Differentially expressed genes in PDAC

Activated and inhibited transcription factors in PDAC

Prognostic values of the identified DEGs in PDAC

Protein-protein interaction (PPI) network

Gene ontology analysis of the DEGs

Pathway enrichment analysis of the DEGs

Discussion

Supplemental Information

DGKH was found to be a prognostic marker for PDAC in three external GEO datasets (GSE21501, GSE50827, and GSE57495).

Kaplan-Meier plots for DGKH created using PROGgeneV2. The patient cohorts were divided into two equal groups based on median expression for DGKH. P<0.05 was accepted as statistically significant.

DOI: 10.7717/peerj.10141/supp-1

The identified up- and down-regulated genes in PDAC.

NS: p≥ 0.05, N/A; not available.

DOI: 10.7717/peerj.10141/supp-2

The predicted transcription factors activated or inhibited in PDAC based on the lists of up-regulated and down-regulated genes resulted from the meta-analysis.

Light colored rows: activated TFs, dark colored row: inhibited TF.

DOI: 10.7717/peerj.10141/supp-3

The results of the Kaplan-Meier survival analysis of the identified DEGs in five external datasets.

NS: nonsignificant, p≥ 0.05; N/A: not available, p: p value, HR: Hazard ratio. Underlined HR values indicate an association with good outcome.

DOI: 10.7717/peerj.10141/supp-4

Enriched categories and corresponding enriched genes for MCODE clusters in the protein-protein interaction network.

DOI: 10.7717/peerj.10141/supp-5

The statistics of the enriched pathways and the leading edge genes.

Lines with white color represent the positively related pathways while lines with gray color represent the negatively related pathways. Size is the number of overlapping genes between categories and the differentially expressed gene list. P<0.05 and FDR<0.05 are accepted as statistically significant. P and/or FDR values <2.220446e-16 were shown as 0e+00. NS: Normalized enrichment score, ES: Enrichment Score, LEN: Leading Edge Number.

DOI: 10.7717/peerj.10141/supp-6

Additional Information and Declarations

Competing Interests

The author declares that they have no competing interests.

Author Contributions

Sevcan Atay conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The data is available at NCBI GEO: GSE62452, GSE15471, GSE62165, GSE56560, GSE21501, GSE50827, GSE57495, GSE71729.

The TCGA-PAAD and TCGA-Pan-cancer raw data is available at UCSC Zena (available at https://xenabrowser.net/datapages/).

Funding

The author received no funding for this work.

35 Citations 4,336 Views 707 Downloads

MIT

Your institution may have Open Access funds available for qualifying authors. See if you qualify

Publish for free

Comment on Articles or Preprints and we'll waive your author fee
Learn more

Five new journals in Chemistry

Free to publish • Peer-reviewed • From PeerJ
Find out more