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TranscriptomicsU2AF1 mutations alter splice site recognition in hematological malignancies
Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 altered its normal role in RNA splicing. W...
ORGANISM(S): Homo sapiens 
2014-09-23 | E-GEOD-58871 | biostudies-arrayexpress
TranscriptomicsWidespread Use of Non-Productive Alternative Splice Sites in Saccharomyces cerevisiae
Using RNA-Seq analysis of nonsense-mediated mRNA decay (NMD) mutant strains, we show that many Saccharomyces cerevisiae intron-containing genes exhibit usage of alternative splice sites, but most transcripts generated by splicing from these sites are non-functional because they introduce premature t...
ORGANISM(S): Saccharomyces cerevisiae BY4741 
2014-02-21 | E-GEOD-55213 | biostudies-arrayexpress
ProteomicsSearching NE-enriched proteomics datasets for splice junction peptides
MudPIT datasets for NaOH-extracted and Salt-and-Detergent (SD)-extracted rat nuclear membranes were obtained from skeletal muscle and liver tissue as described in the following references: Wilkie GS, Korfali N, Swanson SK, Malik P, Srsen V, Batrakou DG, de las Heras J, Zuleger N, Kerr AR, Florens L,...
ORGANISM(S): Rattus Norvegicus (ncbitaxon:10116) 
2018-01-18 | MSV000081951 | MassIVE
TranscriptomicsA Novel Androgen Receptor Splice Variant Is Upregulated during Prostate Cancer Progression
The androgen receptor (AR) plays a key role in progression to incurable androgen-ablation resistant prostate cancer (PCA). We have identified three novel AR splice variants lacking the ligand binding domain (designated as AR3, AR4 and AR5) in hormone insensitive PCA cells. AR3, one of the major spl...
ORGANISM(S): Homo sapiens 
2009-03-16 | E-GEOD-13919 | biostudies-arrayexpress
TranscriptomicsRNA-seq of rat dorsal root ganglia after ligation to investigate central nervous system transcriptomics in chronic pain using agnostic splice site discovery methods
The study pursued dual goals: To advance mRNA-seq bioinformatics towards unbiased transcriptome capture and to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We found that 12.4% of known genes were induced and 7% were sup...
ORGANISM(S): Rattus norvegicus 
2010-05-01 | E-GEOD-20895 | biostudies-arrayexpress
TranscriptomicsNuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans
We have recently shown that transcription initiation RNAs (tiRNAs) are derived from sequences downstream of transcription start sites. Here we report the identification of a second class of nuclear-specific ~17-18 nucleotide small RNA whose 3M-bM-^@M-^Y ends map precisely to the splice donor site of...
ORGANISM(S): Homo sapiens 
2010-07-01 | E-GEOD-20664 | biostudies-arrayexpress
TranscriptomicsIdentification of differentially regulated splice variants and novel exons in glial brain tumors using exon arrays
Aberrant splice variants are involved in the initiation and/or progression of glial brain tumors. We therefore set out to identify splice variants that are differentially expressed between histological subgroups of gliomas. Splice variants were identified using a novel platform that profiles the exp...
ORGANISM(S): Homo sapiens 
2008-01-28 | E-GEOD-9385 | biostudies-arrayexpress
GenomicsPrediction and quantification of splice events from RNA-seq data
Analysis of splice variants from short read RNA-seq data remains a challenging problem. Here we present a novel method for the genome-guided prediction and quantification of splice events from RNA-seq data, which enables the analysis of unannotated and complex splice events. Splice junctions and exo...
EGAS00001001026 | EGA
ProteomicsIdentification of differentially expressed splice variants by the proteogenomic pipeline SPLICIFY
Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant spli...
ORGANISM(S): Homo sapiens (Human) 
2017-07-28 | PXD006486 | Pride
Human Proteogenomics Splicing Crc Label-free Colorectal cancer 
TranscriptomicsA Splice Variant of HER2 Activates Key Signaling Cascades and Evokes Mammary Tumors and Metastases
The Epidermal Growth Factor Receptor 2 (ERBB2 or HER2) is amplified and overexpressed in approximately 20% of invasive breast cancers and is associated with metastasis and poor prognosis. Here we describe the role of a constitutively active splice variant of HER2 (Delta-HER2) in human mammary epithe...
ORGANISM(S): Homo sapiens 
2013-10-22 | E-GEOD-42781 | biostudies-arrayexpress
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