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Fig. 1 | BMC Medical Genomics

Fig. 1

From: Integrated analysis of omics data using microRNA-target mRNA network and PPI network reveals regulation of Gnai1 function in the spinal cord of Ews/Ewsr1 KO mice

Fig. 1

Illustration of the workflow of the pipeline. Transcription factor (TF) gene has multiple functions to regulate transcription. Generated mRNAs are regulated by microRNA and translated proteins have functions with interacted proteins and molecules. RNA sequencing data and microRNA (miRNA) microarray data are generated from spinal cord extraction in Ews/Ewsr1 knockout and wild type mice. SAM (Significance Analysis of Microarrays) is used for selection of significantly expressed miRNA from miRNA microarrays. TargetScan and miRDB were used to predict target genes of miRNAs. From RNA sequencing data, gene expression values are mapped to the reference genome data using Tophat. Then negative correlated differentially expressed genes (DEGs) are selected. Significantly expressed microRNA target genes have many interacting proteins. Specific target gene interactional neighbor proteins are searched in the STRING DB. PPI network analyzed with gene expression value. Analysis results of miRNA-mRNA network and PPI network are integrated by analyzing correlation in expression levels. Regulated genes further are analyzed and visualized with DAVID, KEGG and Cytoscape

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BMC Medical Genomics

ISSN: 1755-8794

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