Predicting the target genes of microRNA based on microarray data

Cao, B.; Ji, Tieming; Zhou, Bin; Zou, Jizhen; Jiao, G.Q.

doi:10.4238/2013.december.2.4

Cited by 5 publications

(2 citation statements)

References 29 publications

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“…MiRNAs are endogenous single-stranded noncoding RNAs (approximately 18–25 nucleotides) that can regulate gene expression through facilitating the degradation or translational repression of target mRNAs via binding to their 3′-untranslated regions [9–11]. In animals, miRNAs are among the most affluent classes of regulators because miRNA genes may regulate up to 60% of protein-coding genes, but only account for 2 to 5% of the total number of all mammalian genes [12–14]. In mouse, over-expression miR-205 increased cellular proliferation and resulted in an expansion of the progenitor-cell population [15].…”

Section: Introductionmentioning

confidence: 99%

Detection and comparison of microRNAs in the caprine mammary gland tissues of colostrum and common milk stages

Hou

Song

et al. 2017

BMC Genet

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BackgroundMicroRNAs (miRNAs) have a great influence on various physiological functions. A lot of high-throughput sequencing (HTS) research on miRNAs has been executed in the caprine mammary gland at different lactation periods (common milk lactation and dry period), but little is known about differentially expressed miRNAs in the caprine mammary gland of colostrum and peak lactation periods.ResultThis study identified 131 differentially expressed miRNAs (P < 0.05 and log2 colostrum normalized expression (NE)/peak lactation NE > 1 or log2 colostrum NE/peak lactation NE < −1), including 57 known miRNAs and 74 potential novel miRNAs in the colostrum and peak lactation libraries. In addition, compared with differentially expressed miRNAs in the peak lactation period, 45 miRNAs in the colostrum lactation period were remarkably upregulated, whereas 86 miRNAs were markedly downregulated (P < 0.05 and log2 colostrum NE/peak lactation NE > 1 or log2 colostrum NE/peak lactation NE < −1). The expressions of 10 randomly selected miRNAs was analyzed through stem-loop real-time quantitative PCR (RT-qPCR). Their expression patterns were the same with Solexa sequencing results. Pathway analysis suggested that oestrogen, endocrine, adipocytokine, oxytocin and MAPK signalling pathways act on the development of mammary gland and milk secretion importantly. In addition, the miRNA-target-network showed that the bta-miR-574 could influence the development of mammary gland and lactation by leptin receptor (LEPR), which was in the adipocytokine signalling pathway. Chr5_3880_mature regulated mammary gland development and lactation through Serine/threonine-protein phosphatase (PPP1CA), which was in the oxytocin signalling pathway.ConclusionsOur finding suggested that the profiles of miRNAs were related to the physiological functions of mammary gland in the colostrum and peak lactation periods. The biological features of these miRNAs may help to clarify the molecular mechanisms of lactation and the development of caprine mammary gland.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-017-0498-2) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Detection and comparison of microRNAs in the caprine mammary gland tissues of colostrum and common milk stages

Hou

Song

et al. 2017

BMC Genet

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“…Via the use of the miRDB website, the putative targets of miRNAs were predicted (Supplementary Tables S2 and S3). Since tools for predicting target genes may cause high false positive and false negative rates [12], we used co-expression method to validate the targets in ESCA. microRNA can degrade and inhibit target gene mRNAs by the specific base pairing, which negatively regulates the expression of target genes [13].…”

Section: Resultsmentioning

confidence: 99%

MicroRNA-550a is associated with muscle system conferring poorer survival for esophageal cancer

Hong

Liu

et al. 2019

Bioscience Reports

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Background Esophageal cancer (ESCA) is one of the most common cancers in the digestive tract. Approximately 300000 people on an average die of ESCA per year worldwide. The determination of key microRNAs for the prognosis of ESCA is of indispensable significance in the clinical treatment. Methods The differentially expressed microRNAs were screened by analyzing The Cancer Genome Atlas (TCGA) database. By using the survival data of the database, we analyzed correlation between patients’ survival time and miR-550a expression levels. Differential expression analysis and gene set enrichment analysis were performed using the targeted data. Results It was found that patients with high miR-550a expression levels had shorter survival time. Data mining and signal pathway enrichment analysis of TCGA database showed that abnormal miR-550a expressions affected the recurrence of tumors by the muscle system regulation. Conclusions Through the proposed investigation, miR-550a is found to be a potential biomarker as well as non-coding therapeutic target for esophagus cancer. These results suggest that miR-550a may serve as a therapeutic target and predictor for ESCA survival.

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MicroRNA target prediction: theory and practice

et al. 2014

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The present study is one of the few that includes tissue samples in the evaluation of target prediction algorithms designed to detect microRNA (miRNA) sequences that might interact with particular messenger RNA (mRNA) sequences. Twelve different target prediction tools were used to find miRNA sequences that might interact with CCL20 gene expression. Different algorithms predicted controversial miRNA sequences for CCL20 regulation due to a different weighting of parameters. Hsa-miR-21 and hsa-miR-145 suggested by four or more programs were chosen for further investigation. Possible real interaction of these miRNA sequences with CCL20 gene expression was monitored using luciferase assays and expression analyses of tissue samples of colorectal adenocarcinoma by either qRT-PCR or ELISA. Folding status of seed-binding sites in complete mRNA and 3'UTR of CCL20 was predicted. Prediction of miRNA expression was attempted based on CCL20 expression data. Eight of the target prediction tools forecasted a role for hsa-miR-21 and four mentioned hsa-miR-145 in CCL20 gene regulation. Laboratory experimentation showed that CCL20 may serve as a target of hsa-miR-21 but not hsa-miR-145. Expression of the molecules resulted in no clear assertion. Folding of seed-binding sites was predicted to be relatively constant for the complete mRNA and 3'UTR. Predicting miRNA expression based on target gene expression was impossible. This might be attributable to the fact that effects of miRNA activity may oscillate between gene product repression and activation. Additional systematic studies are needed to address this issue.

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Predicting the target genes of microRNA based on microarray data

Cited by 5 publications

References 29 publications

Detection and comparison of microRNAs in the caprine mammary gland tissues of colostrum and common milk stages

Detection and comparison of microRNAs in the caprine mammary gland tissues of colostrum and common milk stages

MicroRNA-550a is associated with muscle system conferring poorer survival for esophageal cancer

MicroRNA target prediction: theory and practice

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