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Genome-wide maps of gene expression in alkaline sphingomyelinase knockout mice

ABSTRACT: Intestinal alkaline sphingomyelinase (alk-SMase) generates ceramide and inactivates platelet-activating factor and associated with digestion and inhibition of cancer. There is few study to analyze the correlated function and characterize the genes related to alk-SMase comprehensively. In this work, deep RNA sequencing was performed to investigate the function of alk-SMase. Our RNA-seq data found 239 differentially expressed mRNAs between the wild type (WT) mice and alk-SMase (gene NPP7) knockout (KO) mice, in which 73 were significantly up-regulated and 166 were down-regulated, including protein coding genes, non-coding RNAs. Notably, the results of gene ontology functional enrichment analysis indicated that differentially expressed genes were functionally associated with the immune response, regulation of cell proliferation and development related terms using DAVID. Additionally, an integrated PPI and KEGG network was chose to study the relationship of differentially expressed genes, it was shown that some modules was significantly related to alk-SMase and with accordance of previously results. We chose 6 of these genes randomly were validated the accuracy of RNA-seq technology using quantitative real-time polymerase chain reaction (qPCR) and 2 genes showed difference significantly (P<0.05).

ORGANISM(S): Mus musculus

PROVIDER: GSE114608 | GEO | 2019/01/01

REPOSITORIES: GEO

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Project description:Intestinal alkaline sphingomyelinase (alk-SMase) generates ceramide and inactivates platelet-activating factor and associated with digestion and inhibition of cancer. There is few study to analyze the correlated function and characterize the genes related to alk-SMase comprehensively. In this work, deep RNA sequencing was performed to investigate the function of alk-SMase. Our RNA-seq data found 239 differentially expressed mRNAs between the wild type (WT) mice and alk-SMase (gene NPP7) knockout (KO) mice, in which 73 were significantly up-regulated and 166 were down-regulated, including protein coding genes, non-coding RNAs. Notably, the results of gene ontology functional enrichment analysis indicated that differentially expressed genes were functionally associated with the immune response, regulation of cell proliferation and development related terms using DAVID. Additionally, an integrated PPI and KEGG network was chose to study the relationship of differentially expressed genes, it was shown that some modules was significantly related to alk-SMase and with accordance of previously results. We chose 6 of these genes randomly were validated the accuracy of RNA-seq technology using quantitative real-time polymerase chain reaction (qPCR) and 2 genes showed difference significantly (P<0.05).

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