Data · collection · 2015
Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing
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MicroRNAs (miRNAs) play key regulatory roles in various biological processes and diseases.
Description
A comprehensive analysis of large scale small RNA sequencing data (smRNA-seq) will be very helpful to explore tissue or disease specific miRNA markers and uncover miRNA variants. Here, we systematically analyzed 410 human smRNA-seq datasets, which samples are from 24 tissue/disease/cell lines.
We tested the mapping strategies and found that it was necessary to make multiple-round mappings with different mismatch parameters. miRNA expression profiles revealed that on average ∼70% of known miRNAs were expressed at low level or not expressed (RPM < 1) in a sample and only ∼9% of known miRNAs were relatively highly expressed (RPM > 100). About 30% known miRNAs were not expressed in all of our used samples. The miRNA expression profiles were compiled into an online database (HMED, bioinfo.life.hust.edu.cn/smallRNA/).
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Dozens of tissue/disease specific miRNAs, disease/control dysregulated miRNAs and miRNAs with arm switching events were discovered. Further, we identified some highly confident editing sites including 24 A-to-I sites and 23 C-to-U sites. About half of them were widespread miRNA editing sites in different tissues.
We characterized that the 2 types of editing sites have different features with regard to location, editing level and frequency. Our analyses for expression profiles, specific miRNA markers, arm switching, and editing sites, may provide valuable information for further studies of miRNA function and biomarker finding.
Links
Where it is published
- Repository landing page tandf.figshare.com/collections/Comprehensive_analysis_of_human_small_RNA_sequenci… ↗
landing page · from DataCite
- Repository landing page tandf.figshare.com/collections/Comprehensive_analysis_of_human_small_RNA_sequenci… ↗
landing page · from DataCite
- DOI doi.org/10.6084/m9.figshare.c.2036852 ↗
DOI / persistent id · from DataCite
- DOI doi.org/10.6084/m9.figshare.c.2036852.v1 ↗
DOI / persistent id · from DataCite
Documentation and papers
Catalogue records · 4
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.c.2036852.v1 ↗
metadata API · from DataCite
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.c.2036852 ↗
metadata API · from DataCite
- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.c.2036852.v1 ↗
catalogue entry · from DataCite
- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.c.2036852 ↗
catalogue entry · from DataCite
Topics
- Stated by source
- Biological sciences · Biological sciences · Health sciences · Health sciences
- From keywords
- Life Sciences · Life Sciences
- Inferred from text
- Disease 75% · RNA sequencing 75% · Sequencing 75%
Provenance · 2 source records, 16 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataCite | 10.6084/m9.figshare.c.2036852 | 13 d ago | JSON v1 |
| DataCite | 10.6084/m9.figshare.c.2036852.v1 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| concepts[disease].local:disease:disease | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].fos:biological-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:biological-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:health-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:health-sciences | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · DataCite | vocabulary-mapper@1.0.0 | keywords['Biological Sciences'] |
| concepts[field].local:field:life-sciences | mapping · DataCite | vocabulary-mapper@1.0.0 | keywords['Biological Sciences'] |
| concepts[modality].local:modality:rna-seq | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · DataCite | connector:datacite@1.0.0 | |
| description | source · DataCite | connector:datacite@1.0.0 | /data/attributes/descriptions |
| license | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| publication_date | source · DataCite | connector:datacite@1.0.0 | /data/attributes/dates |
| title | source · DataCite | connector:datacite@1.0.0 | /data/attributes/titles/0/title |
| updated_date | source · DataCite | connector:datacite@1.0.0 |