RETRACTED ARTICLE: Reanalysis of the gene expression profile in chronic pancreatitis via bioinformatics methods

Abstract

BackgroundDiagnosis at an early stage of chronic pancreatitis (CP) is challenging. It has been reported that microRNAs (miRNAs) are increasingly found and applied as targets for the diagnosis and treatment of various cancers. However, to the best of our knowledge, few published papers have described the role of miRNAs in the diagnosis of CP.MethodWe downloaded gene expression profile data from the Gene Expression Omnibus and identified differentially expressed genes (DEGs) between CP and normal samples of Harlan mice and Jackson Laboratory mice. Common DEGs were filtered out, and the semantic similarities of gene classes were calculated using the GOSemSim software package. The gene class with the highest functional consistency was selected, and then the Lists2Networks web-based system was used to analyse regulatory relationships between miRNAs and gene classes. The functional enrichment of the gene classes was assessed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway annotation terms.ResultsA total of 405 common upregulated DEGs and 7 common downregulated DEGs were extracted from the two kinds of mice. Gene cluster D was selected from the common upregulated DEGs because it had the highest semantic similarity. miRNA 124a (miR-124a) was found to have a significant regulatory relationship with cluster D, and DEGs such as CHSY1 and ABCC4 were found to be regulated by miR-124a. The GO term of response to DNA damage stimulus and the pathway of Escherichia coli infection were significantly enriched in cluster D.ConclusionDNA damage and E. coli infection might play important roles in CP pathogenesis. In addition, miR-124a might be a potential target for the diagnosis and treatment of CP.

Melittin inhibits proliferation, migration and invasion of bladder cancer cells by regulating key genes based on bioinformatics and experimental assays

“…17,18 In fact, many gene expression profiles involved in various aspects cancers have been documented. [19][20][21] However, additional critical genes and pathways associated with BC remain to be investigated.…”

“…In recent years, microarrays employing high‐throughput platforms have emerged as a promising and effective approach for the detection of important genetic or epigenetic alterations in carcinogenesis and identification of promising biomarkers for the diagnosis and prognosis of cancers . In fact, many gene expression profiles involved in various aspects cancers have been documented . However, additional critical genes and pathways associated with BC remain to be investigated.…”

Transcriptome‐wide association study identifies multiple genes and pathways associated with pancreatic cancer

“…Consistent with the result of TWAS, previous studies have reported 4 of the 19 genes (PPP2R2A, E2F3, KCNK5, and SOX4) play important roles in the development of PC, 20-23 and 2 of the 19 genes (CHSY1 and EGLN3) have been proved associated with PC via bioinformatics methods. 25,26 SOX4 is significantly associated with PC and overexpressed in PC patients. Furthermore, it is interesting that the significant SNP rs12530233 of SOX4 gene is an eQTL, suggesting the importance of rs12530233 in the dysfunction of SOX4 expression regulation during the development of PC.…”

Contribution of bioinformatics prediction in microRNA-based cancer therapeutics

“…Bioinformatics approaches have been developed to analyze gene expression profiles in pancreatic cancer to identify the role of miRNAs in early diagnosis and treatment [104]. Similar strategy was developed to analyze gene expression profile in chronic pancreatitis and identify the role of miRNAs in early diagnosis and treatment [105]. The gene expression data was downloaded from Gene Expression Omnibus and differential gene expression analysis was performed to identify differentially expressed genes in mice.…”

“…The miRNAs targeting the differentially regulated genes were identified based on regulatory relationship between miRNAs and genes. The authors identified miR-124a as a potential target for the diagnosis and treatment of chronic pancreatitis [105]. The differential gene expression studies were also able to distinguish between pancreatic adenocarcinoma from normal and chronic pancreatitis [106].…”