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Tumor Biology

, Volume 36, Issue 4, pp 2249–2255 | Cite as

RETRACTED ARTICLE: Identification of core miRNA based on small RNA-seq and RNA-seq for colorectal cancer by bioinformatics

  • Youwei Kou
  • Lei Qiao
  • Qiang Wang
Research Article

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.

Keywords

RNA-seq MicroRNAs Molecular mechanism 

Notes

Conflicts of interest

None.

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Copyright information

© International Society of Oncology and BioMarkers (ISOBM) 2014

Authors and Affiliations

  1. 1.Department of Gastrointestinal and Nutriology SurgeryShengjing Hospital of China Medical UniversityShenyangChina
  2. 2.Department of Colorectal Surgery and OncologyShengjing Hospital of China Medical UniversityShenyangChina

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