Validation of the differential expression pattern of miRNA species by RT-qPCR analysis.

<p>RT-qPCR analysis was performed to quantify the expression levels of miR-122, 126, 145, 24, 106b, 103, 696 and 15b. </p

Length distributions of reads.

<p>A: The data of <i>ob/ob</i> mouse liver samples. B: The data of wild-type mouse liver samples.</p

The abundance of miRNAs in <i>ob/ob</i> mouse liver.

<p>These miRNAs are abundantly expressed in <i>ob/ob</i> mouse liver <i>vs</i>. WT mouse liver (> 13.8% in the total). They are estimated based on the most abundant isomiR and sum of all isomiRs, respectively. A: up-regulated miRNAs, B: down-regulated miRNAs. </p

The flowchart to analyze miRNA/isomiR in the study.

<p>The flowchart to analyze miRNA/isomiR in the study.</p

Expression distribution of rates of dominant isomiRs across different groups.

<p>The <i>F</i> statistic and <i>P</i> values are also presented using ANOVA analysis among different groups. F-nt: female-UCEC-nt; F-tn: female-UCEC-tn; M-nt: male-PRAD-nt; M-tn: male-PRAD-tn; Mix-nt-1: mixed-LUSC-nt; Mix-tn-1: mixed-LUSC-tn; Mix-nt-2: mixed-THCA-nt; Mix-tn-2: mixed-THCA-tn. The blue bar indicates the rate of the most dominant isomiR and the secondary dominant isomiR, the red bar indicates the rate of the most dominant isomiR and the third dominant isomiR, and the green bar indicated the rate of the most dominant isomiR and the fourth dominant isomiR.</p

The top 5 gene categories based on target mRNAs of related miRNAs.

<p>The top 5 gene categories, including biological process, cellular component and molecular function, are presented according to target mRNAs of (A) miR-23ab, (B) miR-24, (C) miR-27ab and (D) the common target mRNAs of the three miRNA gene families.</p

A Comprehensive Analysis of miRNA/isomiR Expression with Gender Difference

<div><p>Although microRNAs (miRNAs) have been widely studied as epigenetic regulation molecules, fewer studies focus on the gender difference at the miRNA and isomiR expression levels. In this study, we aim to understand the potential relationships between gender difference and miRNA/isomiR expression through a comprehensive analysis of small RNA-sequencing datasets based on different human diseases and tissues. Based on specific samples from males and females, we determined that some miRNAs may be diversely expressed between different tissues and genders. Thus, these miRNAs may exhibit inconsistent and even opposite expression between males and females. According to deregulated miRNA expression profiles, some dominantly expressed miRNA loci were selected to analyze isomiR expression patterns using rates of dominant isomiRs. In some miRNA loci, isomiRs showed statistical significance between tumor and normal samples and between males and females samples, suggesting that isomiR expression patterns are not always invariable but may vary between males and females, as well as among different tissues, tumors, and normal samples. The divergence implicates the fluctuation in the expression of miRNA and its detailed expression at the isomiR levels. The divergence also indicates that gender difference may be an important factor that affects the screening of disease-associated miRNAs and isomiRs. This study suggests that miRNA/isomiR expression and gender difference may be more complex than previously assumed and should be further studied according to specific samples from males or females.</p></div

Distributions of deregulated miRNAs in the 4 kinds of diseases.

<p>A: UCEC; B: PRAD; C: LUSC; D: THCA.</p

Sequencing datasets from the TCGA database are analyzed.

<p>TN: Tumor, Matched Normal. NT: Normal, Matched Tumor.</p><p>Sequencing datasets from the TCGA database are analyzed.</p

Statistical analysis between paired tumor and normal samples or male and female samples using <i>t</i> test in Fig 4.

<p>Statistical analysis between paired tumor and normal samples or male and female samples using <i>t</i> test in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154955#pone.0154955.g004" target="_blank">Fig 4</a>.</p