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  • Title: Identification of core miRNA based on small RNA-seq and RNA-seq for colorectal cancer by bioinformatics.
    Author: Kou Y, Qiao L, Wang Q.
    Journal: Tumour Biol; 2015 Apr; 36(4):2249-55. PubMed ID: 25412953.
    Abstract:
    We aimed to identify the potential microRNA (miRNA) targets for colorectal cancer (CRC). Small RNA-seq and RNA-seq data of GSE46622 were downloaded from Gene Expression Omnibus (GEO) database, including samples of tumor tissue, metastasis tissue, and normal tissue from eight CRC patients. Data comparison of small RNA-seq and RNA-seq was performed through Bowtie and TopHat softwares, respectively. Then the expressed values of each sample were calculated by Cufflinks and Cuffdiff based on fragments per kilobase of exon per millionfragments mapped (FPKM) methods. The differentially expressed miRNAs and core miRNAs were identified by paired t-test. Besides, miRNA target genes were integrated through miRanda, MirTarget2, PicTar, PITI, TargetScan, and miRecords databases, followed by functional analysis of specific miRNA. The average comparison rate of sequence reads in miRNA, noncoding RNA, and other areas of the genome is 49.75, 2.90, and 47.35 %, respectively. A total of 49 miRNAs was differentially expressed. Compared with normal controls, 3 miRNAs were upregulated and 13 miRNAs were downregulated in tumor samples as well as 48 miRNAs were upregulated and 20 miRNAs were downregulated in the metastasis samples. Among them, 18 metastasis-specific expressed miRNAs, 2 tumor-specific expressed miRNAs, and 11 normal expressed miRNA were found. miRNA-1, miRNA-338-5p, miRNA-326, and miR-490-5p were selected as important miRNAs. Besides, miRNA-338-5p target gene RAB6B, FAP, and CTGF were identified as oncogenes. The miRNAs, such as miRNA-1, miRNA-338-5p, and miRNA-326 may be used as potential targets for CRC diagnosis and treatment.
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