Identification of key genes and associated pathways in KIT/PDGFRA wild‑type gastrointestinal stromal tumors through bioinformatics analysis

Molecular Medicine Reports
Wen-Jie WangHong-Bin Liu

Abstract

Gastrointestinal stromal tumors (GISTs) are the most common type of mesenchymal tumor in the gastrointestinal tract. The present study aimed to identify the potential candidate biomarkers that may be involved in the pathogenesis and progression of v‑kit Hardy‑Zuckerman 4 feline sarcoma viral oncogene homolog (KIT)/platelet‑derived growth factor receptor α (PDGFRA) wild‑type GISTs. A joint bioinformatics analysis was performed to identify the differentially expressed genes (DEGs) in wild‑type GIST samples compared with KIT/PDGFRA mutant GIST samples. Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs was conducted using Database for Annotation, Visualization and Integrated Discovery and KEGG Orthology‑Based Annotation System (KOBAS) online tools, respectively. Protein‑protein interaction (PPI) networks of the DEGs were constructed using Search Tool for the Retrieval of Interacting Genes online tool and Cytoscape, and divided into sub‑networks using the Molecular Complex Detection (MCODE) plug‑in. Furthermore, enrichment analysis of DEGs in the modules was analyzed with KOBAS. In total, 546 DEGs were identified, including 238 upregulated genes primarily enriched in 'cell ...Continue Reading

References

Jan 11, 2003·Science·Michael C HeinrichJonathan A Fletcher
Jan 15, 2003·BMC Bioinformatics·Gary D Bader, Christopher W V Hogue
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
May 22, 2007·Lancet·Suzanne A Eccles, Danny R Welch
Jun 14, 2008·Proceedings of the National Academy of Sciences of the United States of America·Chi TarnAndrew K Godwin
Aug 19, 2008·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Avo ArtinyanJoshua D I Ellenhorn
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Sep 10, 2009·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Roopali RoyMarsha A Moses
Dec 17, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Ann W GramzaMichael C Heinrich
Jun 16, 2010·Laboratory Investigation; a Journal of Technical Methods and Pathology·Annalisa AstolfiGuido Biasco
Oct 6, 2011·Archives of Pathology & Laboratory Medicine·Deepa T Patil, Brian P Rubin
Nov 18, 2011·Nature Reviews. Cancer·Christopher L CorlessMichael C Heinrich
Nov 26, 2013·Lancet·Heikki Joensuu, Peter Hohenberger
Dec 19, 2014·BMC Systems Biology·Chia-Hao ChinChung-Yen Lin
May 10, 2016·Lancet·Eric Van CutsemHans Prenen
Jul 21, 2016·Hereditary Cancer in Clinical Practice·Riccardo Ricci
Jul 28, 2016·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Ryuji YamaguchiKiichi Hirota
Dec 8, 2016·Nucleic Acids Research·Damian SzklarczykChristian von Mering

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Citations

Feb 3, 2021·Diagnostics·Iva BrčićBernadette Liegl-Atzwanger
Jan 10, 2021·International Journal of Molecular Sciences·Christos VallilasMichalis V Karamouzis

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Datasets Mentioned

BETA
GSE20708
GPL570
GSE17743

Methods Mentioned

BETA
GTPase
chip

Software Mentioned

Hclust
ClueGO
BiNGO
KOBAS
Molecular Complex Detection ( MCODE )
affy
sva
pheatmap
Cytoscape
limma

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