YM500v3: a database for small RNA sequencing in human cancer research

Abstract

We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis. We have also incorporated >10 000 cancer-related RNA-seq and >3000 more smRNA-seq data sets into the YM500v3 database. Furthermore, there are two main new sections, ‘Survival' and ‘Cancer', in this updated version. The ‘Survival’ section provides the survival analysis results in all cancer types or in a user-defined group of samples for a specific sncRNA. The ‘Cancer’ section provides the results of differential expression analyses, miRNA–gene interactions and cancer miRNA-related pathways. In the ‘Expression’ section, sncRNA expression profiles across cancer and sample types are newly provided. Cancer-related sncRNAs hold potential for both biotech applications and basic research.

RAB27B‐activated secretion of stem‐like tumor exosomes delivers the biomarker microRNA‐146a‐5p, which promotes tumorigenesis and associates with an immunosuppressive tumor microenvironment in colorectal cancer

“…We used our in‐house pipelines used in previous studies to estimate the expression levels of miRNAs, identify their downstream target genes and annotate their functions . The reads per million (RPM) were used for normalization.…”

Regulation of miRNA Biogenesis and Histone Modification by K63-Polyubiquitinated DDX17 Controls Cancer Stem-like Features

“…The validated and predicated miRNA-gene relationships in this study were based on the pipeline constructed in our previous study (26). In brief, data of experimentally validated miRNAgene interactions were extracted and identified from miRTAR-Base (27), a curated database of miRNA-target interactions.…”

SEA: The small RNA Expression Atlas

“…Results are provided in an interactive manner, such as sncRNA locus sorting and filtering by biological features. All annotation and expression information are downloadable and accessible as UCSC 4 genome browser tracks; miratlas (Vitsios et al, 2017) allows for searching miRNA expression profiles as well as sRNA-seq experiments and provides information on the miRNA modification analysis; and YM500v3 (Chung et al, 2017) provides interactive web reports on sRNA expression profiles, sRNA differential expression and miRNA gene targets.…”

“…Except YM500v3 (Chung et al, 2017), current tools do not provide miRNAs and gene targets, of note YM500v3 is only limited to cancer miRNome studies. Also, there is currently no web application that allows for the identification of biomarkers of disease via machine-learning.…”

“…A detailed comparison of SEA to other existing sRNA expression databases (Table 2) highlights that SEA is superior in terms of supported organism, annotations, diseases, tissues, sRNA based classification, pathogen k-mer DE, known miRNA disease associations, user specific experimental data upload, cross study comparisons and re-analysis with selected samples. SEA contains over 4200 samples in its database, which is considerably less than YM500v3 (Chung et al, 2017), which hosts over 8000 cancer samples. It is to be noted, however, that the YM500v3 database only supports cancer datasets and no other disease types (Table 2).…”