MiRNA guidelines
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To the miRNA guidelines summary
all annotations to PMID:22269326
pdf of presentation File:GOCmiRNA2014.pdf
Consortium minutes [1]
Discussion to include annotation of other non-coding RNAs
Summary of MOD miRNA annotations
MOD/database | Brief summary of progress | Attending meeting |
TAIR | Have been creating Arabidopsis miRNAs annotations for years. 199 miRNA genes so far, 228 annotations to 'gene silencing by miRNA' or kids, for the 73 experimental annotations, mostly IDA, IMP, IGI but also a few IEP | Tanya/Donghui |
Wormbase | Mostly focused on miRNA annotations for the greatest hits of C. elegans miRNAs, namely let-7, lin-4, lsy-6, etc. Our BP annotations to the miRNAs have included the cellular level processes they control and also the organismal level processes that they, in turn, regulate, e.g. heterochronic development, neuronal fate specification, etc. We also have some MF annotations for their mRNA binding activities. Users have recently ask us about including these types of annotations in GO. We haven't yet considered making IEP annotations for miRNAs but I'm glad you raised that issue again. | Kimberley |
GOA/UCL | Waiting for human microRNA identifiers, due Spring 2014 | Ruth/Rachael |
RGD | We currently take ISO annotations for rat orthologs from mouse and human miRNA-related genes. Our curation prioritization is disease-centric so as miRNAs come up as related to the disease category we are covering we will curate them. We also may do a focused effort to curate miRNAs and their targets at some point. | Jennifer |
MGI | Have been creating mouse miRNAs annotations for years | |
Dicty | not a priority at the moment | |
ZFIN | currently has 124 microRNA genes annotated with 260 non-ND evidence annotations using 69 distinct GO terms. | Doug |
PomBase | Pombe also has lots of antisense RNAs which do not get cleaved into siRNA but are presumed to regulate the gene they are antisense to | Val |
Agenda
- Agree what to focus meeting on
- microRNAs
- siRNAs
- lncRNAs
- Annotation of function wrt regulation of gene expression, chromatin modification etc
- transcription/translation targets
- downstream effects
- example papers: how to annotate PMID:22269326 survey monkey questions suggested miRNA annotations short version of miRNA annotations
- use of IEP evidence code example paper PMID:21993888 annotation of differentially expressed miRNAs
Should differential expression of miRNAs in specific cell types/conditions be captured in GO Is Table 1 IEP data or IDA?
- use of existing database information
Current stats
No. annotations to "gene silencing by miRNA" or child terms;
UniProtKB(295) TAIR(228) ZFIN(144) RGD(96) MGI(84) FB(76) AspGD(15) CGD(1) dictyBase(1)
Other information
Discussion to include annotation of other non-coding RNAs (siRNAs, lncRNAs (long non-coding RNAs)) with roles in regulation of transcription, translation, stability of mRNA, chromatin silencing, chromatin organisation.
microRNA and siRNA comparison table
lncRNAs (long non-coding RNAs) review
siRNA role in immunity review