ArticleDatabase : the journal of biological databases and curation2017
SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets.
Article in Database : the journal of biological databases and curation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 15 citations in OpenAlex.
- Deciphering splicing heterogeneity at single-cell resolution by SCSES.Nature communications · 2025Article
- miR-448-3p/miR-1264-3p Participates in Intermittent Hypoxic Response in Hippocampus by Regulating Fam76b/hnRNPA2B1.CNS neuroscience & therapeutics · 2025Article
- Dysregulation of alternative splicing in spinocerebellar ataxia type 1.Human molecular genetics · 2024Article
- Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2021Article
- Integrated analysis of a compendium of RNA-Seq datasets for splicing factors.Scientific data · 2020Article
- A data mining paradigm for identifying key factors in biological processes using gene expression data.Scientific reports · 2018Article
- Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis.Scientific reports · 2018Article
- RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins.Database : the journal of biological databases and curation · 2018Article
- GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata.Database : the journal of biological databases and curation · 2018Article
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Authors and funding
8 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although the number of RNA-Seq datasets deposited publicly has increased over the past few years, incomplete annotation of the associated metadata limits their potential use. Because of the importance of RNA splicing in diseases and biological processes, we constructed a database called SFMetaDB by curating datasets related with RNA splicing factors. Our effort focused on the RNA-Seq datasets in which splicing factors were knocked-down, knocked-out or over-expressed, leading to 75 datasets corresponding to 56 splicing factors. These datasets can be used in differential alternative splicing analysis for the identification of the potential targets of these splicing factors and other functional studies. Surprisingly, only ∼15% of all the splicing factors have been studied by loss- or gain-of-function experiments using RNA-Seq. In particular, splicing factors with domains from a few dominant Pfam domain families have not been studied. This suggests a significant gap that needs to be addressed to fully elucidate the splicing regulatory landscape. Indeed, there are already mouse models available for ∼20 of the unstudied splicing factors, and it can be a fruitful research direction to study these splicing factors in vitro and in vivo using RNA-Seq. Database URL:http://sfmetadb.ece.tamu.edu/
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