Dataset Information

Analyses of a Panel of Transcripts Identified From a Small Sample Size and Construction of RNA Networks in Hepatocellular Carcinoma.

ABSTRACT: Hepatocellular carcinoma (HCC) is one of the most common cancers in the world. Dysregulation of mRNAs and non-coding RNAs (ncRNAs) plays critical roles in the progression of HCC. Here, we investigated HCC samples by RNA-seq and identified a series of dysregulated RNAs in HCC. Various bioinformatics analyses established long non-coding RNA (lncRNA)-mRNA co-expression and competing endogenous RNA (ceRNA) networks in circRNA-miRNA-mRNA axis, indicating the potential cis and/or trans regulatory roles of lncRNAs and circRNAs. Moreover, GO pathway analysis showed that these identified RNAs were associated with many biological processes that were related to tumorigenesis and tumor progression. In conclusion, we systematically established functional networks of lncRNA-mRNA, circRNA-miRNA-mRNA to further unveil the potential interactions and biological processes in HCC. These results provide further insights into gene expression network of HCC and may assist future diagnosis of HCC.

SUBMITTER: Sheng Z

PROVIDER: S-EPMC6530380 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Analyses of a Panel of Transcripts Identified From a Small Sample Size and Construction of RNA Networks in Hepatocellular Carcinoma.

Sheng Zhiyong Z Wang Xiaolin X Xu Geliang G Shan Ge G Chen Liang L

Frontiers in genetics 20190508

Hepatocellular carcinoma (HCC) is one of the most common cancers in the world. Dysregulation of mRNAs and non-coding RNAs (ncRNAs) plays critical roles in the progression of HCC. Here, we investigated HCC samples by RNA-seq and identified a series of dysregulated RNAs in HCC. Various bioinformatics analyses established long non-coding RNA (lncRNA)-mRNA co-expression and competing endogenous RNA (ceRNA) networks in circRNA-miRNA-mRNA axis, indicating the potential <i>cis</i> and/or <i>trans</i> r ...[more]

PMID: 31156698

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Project description:BackgroundRecent work using large datasets (>500 records per subject) has demonstrated seemingly high levels of step-to-step variation in peak plantar pressure within human individuals during walking. One intuitive consequence of this variation is that smaller sample sizes (e.g., 10 steps per subject) may be quantitatively and qualitatively inaccurate and fail to capture the variance in plantar pressure of individuals seen in larger data sets. However, this remains quantitatively unexplored reflecting a lack of detailed investigation of intra-subject sample size effects in plantar pressure analysis.MethodsHere we explore the sensitivity of various plantar pressure metrics to intra-subject sample size (number of steps per subject) using a random subsampling analysis. We randomly and incrementally subsample large data sets (>500 steps per subject) to compare variability in three metric types at sample sizes of 5-400 records: (1) overall whole-record mean and maximum pressure; (2) single-pixel values from five locations across the foot; and (3) the sum of pixel-level variability (measured by mean square error, MSE) from the whole plantar surface.ResultsOur results indicate that the central tendency of whole-record mean and maximum pressure within and across subjects show only minor sensitivity to sample size >200 steps. However, <200 steps, and particularly <50 steps, the range of overall mean and maximum pressure values yielded by our subsampling analysis increased considerably resulting in potential qualitative error in analyses of pressure changes with speed within-subjects and in comparisons of relative pressure magnitudes across subjects at a given speed. Our analysis revealed considerable variability in the absolute and relative response of the single pixel centroids of five regions to random subsampling. As the number of steps analysed decreased, the absolute value ranges were highest in the areas of highest pressure (medial forefoot and hallux), while the largest relative changes were seen in areas of lower pressure (the midfoot). Our pixel-level measure of variability by MSE across the whole-foot was highly sensitive to our manipulation of sample size, such that the range in MSE was exponentially larger in smaller subsamples. Random subsampling showed that the range in pixel-level MSE only came within 5% of the overall sample size in subsamples of >400 steps. The range in pixel-level MSE at low subsamples (<50) was 25-75% higher than that of the full datasets of >500 pressure records per subject. Overall, therefore, we demonstrate a high probability that the very small sample sizes (n < 20 records), which are routinely used in human and animal studies, capture a relatively low proportion of variance evident in larger plantar pressure data set, and thus may not accurately reflect the true population mean.

Dataset Information

Analyses of a Panel of Transcripts Identified From a Small Sample Size and Construction of RNA Networks in Hepatocellular Carcinoma.

Publications

Analyses of a Panel of Transcripts Identified From a Small Sample Size and Construction of RNA Networks in Hepatocellular Carcinoma.

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