ArticleGenome research2014
Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- NOVA1 inhibition by miR-146b-5p in the remnant tissue microenvironment defines occult residual disease after gastric cancer removal.Oncotarget · 2016Trial
- MYCN and helicases DDX17 and DDX5 have opposite effects on the production of readthrough-associated chimeric transcripts.Cellular and molecular life sciences : CMLS · 2026Article
- NOVA1 Activation Modulates the Tumor Immune Microenvironment through STING Phosphorylation in Head and Neck Squamous Cell Carcinoma.Cancer research and treatment · 2026Article
- A transcriptomic and proteomic map of primary human cell types.Nucleic acids research · 2026Article
- Article
- Alternative splicing in EMT and TGF-β signaling during cancer progression.Seminars in cancer biology · 2024Review
- SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors.Database : the journal of biological databases and curation · 2023Article
- Epithelial specific splicing regulator proteins as emerging oncogenes in aggressive prostate cancer.Oncogene · 2023Review
- Stimuli-Responsive Polysaccharide Hydrogels and Their Composites for Wound Healing Applications.Polymers · 2023Review
- Modulation of alternative splicing during early infection of human primary B lymphocytes with Epstein-Barr virus (EBV): a novel function for the viral EBNA-LP protein.Nucleic acids research · 2021Article
- FGF-2 promotes angiogenesis through a SRSF1/SRSF3/SRPK1-dependent axis that controls VEGFR1 splicing in endothelial cells.BMC biology · 2021Article
- CD44 alternative splicing senses intragenic DNA methylation in tumors via direct and indirect mechanisms.Nucleic acids research · 2021Article
- Graphitic Carbon Nitride Causes Widespread Global Molecular Changes in Epithelial and Fibroblast Cells.ACS omega · 2021Article
- MeDAS: a Metazoan Developmental Alternative Splicing database.Nucleic acids research · 2021Article
- Alternative splicing in endothelial cells: novel therapeutic opportunities in cancer angiogenesis.Journal of experimental & clinical cancer research : CR · 2020Review
- miR-27-3p inhibition restore fibroblasts viability in diabetic wound by targeting NOVA1.Aging · 2020Article
- Intragenic recruitment of NF-κB drives splicing modifications upon activation by the oncogene Tax of HTLV-1.Nature communications · 2020Article
- Characterizing the interplay between gene nucleotide composition bias and splicing.Genome biology · 2019Article
- Influence of Cell Type and Culture Medium on Determining Cancer Selectivity of Cold Atmospheric Plasma Treatment.Cancers · 2019Article
- NOVA1 induction by inflammation and NOVA1 suppression by epigenetic regulation in head and neck squamous cell carcinoma.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing is the main mechanism of increasing the proteome diversity coded by a limited number of genes. It is well established that different tissues or organs express different splicing variants. However, organs are composed of common major cell types, including fibroblasts, epithelial, and endothelial cells. By analyzing large-scale data sets generated by The ENCODE Project Consortium and after extensive RT-PCR validation, we demonstrate that each of the three major cell types expresses a specific splicing program independently of its organ origin. Furthermore, by analyzing splicing factor expression across samples, publicly available splicing factor binding site data sets (CLIP-seq), and exon array data sets after splicing factor depletion, we identified several splicing factors, including ESRP1 and 2, MBNL1, NOVA1, PTBP1, and RBFOX2, that contribute to establishing these cell type-specific splicing programs. All of the analyzed data sets are freely available in a user-friendly web interface named FasterDB, which describes all known splicing variants of human and mouse genes and their splicing patterns across several dozens of normal and cancer cells as well as across tissues. Information regarding splicing factors that potentially contribute to individual exon regulation is also provided via a dedicated CLIP-seq and exon array data visualization interface. To the best of our knowledge, FasterDB is the first database integrating such a variety of large-scale data sets to enable functional genomics analyses at exon-level resolution.
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Registered trials
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