Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA131295 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:SRp20 regulates Genome-wide Alternative RNA splicing events in U2OS cells
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Project description:We used Affymetrix GeneChipM-BM-. Human Exon 1.0 ST Arrays to identify alternative splicing events in 15 samples of PDAC compared to 6 non-tumor samples. Several commercial and open source software approaches for the analysis of differential splicing were tested and a subset of overlapping results was validated using RT-PCR and sequencing. Splicing variants could be validated in several genes closely related to cancer. Pathway analysis of genes predicted to be alternatively spliced revealed an enrichment of genes in categories closely related to cell-cell interactions and kinase activity. 15 samples of pancreatic ductal adenocarcinoma and 6 non tumor pancreatic samples were analyzed for alternative splicing events
2013-08-01 | E-GEOD-23397 | biostudies-arrayexpress
Project description:Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (HJAY)
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Project description:Determining the impact of alternative splicing events on transcriptome dynamics
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Project description:High throughput sequencing identifies alternative splicing events regulated by PRMT9
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Project description:Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (Exon array)
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Project description:The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate alternative splicing events
| PRJNA118751 | ENA
Project description:Alternative mRNA splicing represents an effective mechanism of regulating gene function and is a key element to increase the coding capacity of the human genome. Today, an increasing number of reports illustrates that aberrant splicing events are common and functionally important for cancer development. However, more comprehensive analyses are warranted to get novel insights into the biology underlying malignancies like e.g. acute myeloid leukemia (AML). Here, we performed a genome-wide screening of splicing events in AML using an exon microarray platform. We analyzed complex karyotype and core binding factor (CBF) AML cases (n=64) in order to evaluate the ability to detect alternative splicing events distinguishing distinct leukemia subgroups. Testing different commercial and open source software tools to compare the respective AML subgroups, we could identify a large number of potentially alternatively spliced transcripts with a certain overlap of the different approaches. Selected candidates were further investigated by PCR and sequence analysis: out of 24 candidate genes studied, we could confirm alternative splice forms in 8 genes of potential pathogenic relevance, such as PRMT1 regulating transcription through histone methylation and participating in DNA damage response, and PTPN6, which encodes for a negative regulator of cell cycle control and apoptosis. In summary, this first large Exon microarray based study demonstrates that transcriptome splicing analysis in AML is feasible but challenging, in particular with regard to the currently available software solutions. Nevertheless, our results show that alternatively spliced candidate genes can be detected, and we provide a guide how to approach such analyses. Exon expression analysis was performed using GeneChip Human Exon 1.0 ST microarrays in 64 AML patients.
2014-12-15 | E-GEOD-21337 | biostudies-arrayexpress
Project description:EventPointer: An effective identification of alternative splicing events using junction arrays
| PRJNA308905 | ENA
Project description:Alternative splicing generates functional diversity in higher organisms through alternative first and last exons, skipped and included exons, intron retentions and alternative donor and acceptor sites. In large-scale microarray studies in human and mouse, emphasis so far has been placed on exon-skip events, leaving the prevalence and importance of other splice types largely unexplored. Using a new human splice variant database and a genome-wide microarray to probes thousands of splice events of each type, we measured differential expression of splice types across 6 pairs of diverse cell lines and validated the database annotation process. Results suggest that splicing in human is more complex than simple exon skip events, which account for a minority of splicing differences. The relative frequency of differential expression of the splice types correlates with what is found by our annotation efforts. In conclusion, alternative splicing in human cells is considerably more complex than the canonical example of the exon-skip. The complementary approaches of genome-wide annotation of alternative splicing in human and design of genome-wide splicing microarrays to measure differential splicing in biological samples provide a powerful high-throughput tool to study the role of alternative splicing in human biology. Keywords: alternative splicing
2007-12-08 | GSE9734 | GEO