The promising novel biomarkers and candidate small molecule drugs in kidney renal clear cell carcinoma: Evidence from bioinformatics analysis of high-throughput data

Molecular Genetics & Genomic Medicine
Bo ZhangYou Lang Zhou

Abstract

Kidney renal clear cell carcinoma (KIRC) is the most common subtype of renal tumor. However, the molecular mechanisms of KIRC pathogenesis remain little known. The purpose of our study was to identify potential key genes related to the occurrence and prognosis of KIRC, which could serve as novel diagnostic and prognostic biomarkers for KIRC. Three gene expression profiles from gene expression omnibus database were integrated to identify differential expressed genes (DEGs) using limma package. Enrichment analysis and PPI construction for these DEGs were performed by bioinformatics tools. We used Gene Expression Profiling Interactive Analysis (GEPIA) database to further analyze the expression and prognostic values of hub genes. The GEPIA database was used to further validate the bioinformatics results. The Connectivity Map was used to identify candidate small molecules that could reverse the gene expression of KIRC. A total of 503 DEGs were obtained. The PPI network with 417 nodes and 1912 interactions was constructed. Go and KEGG pathway analysis revealed that these DEGs were most significantly enriched in excretion and valine, leucine, and isoleucine degradation, respectively. Six DEGs with high degree of connectivity (ACAA1, A...Continue Reading

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Citations

Jun 13, 2020·The Journal of International Medical Research·Xin-da SongYang Hong
Dec 22, 2020·Frontiers in Molecular Biosciences·Ji-Li Xu, Yong Guo
Jul 9, 2021·Frontiers in Genetics·Yanli WangYang Cao

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Datasets Mentioned

BETA
GSE100666
GSE6344
GPL16951

Software Mentioned

MCODE
affy
Networks Gene Oncology tool ( BiNGO )
cBioPortal
Bioconductor
DAVID ( Database for Annotation Visualization and Integrated D...
DAVID
Gene Expression Profiling Interactive Analysis ( GEPIA )
Limma
Search Tool for the Retrieval

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