[PDF] Top 20 KISSPLICE: de-novo calling alternative splicing events from RNA-seq data
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KISSPLICE: de-novo calling alternative splicing events from RNA-seq data
... in RNA-seq ...(alternative splicing) that produces several alternative transcripts for a same gene, ii) SNPs (single nucleotide polymorphism) that may also produce several transcripts ... Voir le document complet
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en fr Analysis of alternative splicing in RNA-Seq data : development and comparison of bioinformatics tools Analyse de l’épissage alternatif dans les données RNAseq : développement et comparaison d’outils bioinformatiques
... skipping events, a natural question which arises when two conditions are compared is to assess if the inclusion level of the exon significantly changed across ...condition-specific events, we again parti- ... Voir le document complet
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RNA Splicing, Cell Signaling and Response to Therapies
... regulated alternative splicing events across human solid ...recurrent alternative splicing switches in tumor samples reveals novel signatures of ...the RNA-Seq data ... Voir le document complet
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Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle
... multiple alternative splicing ...describing alternative splicing events in the DMD gene since its discovery in 1986 (Supplementary Table ...these data derive from studies ... Voir le document complet
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Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution
... such splicing might be regulated, and some studies have concluded that NAGNAG splicing is purely stochastic and ...deep RNA-Seq data from 16 human and eight mouse tissues to ... Voir le document complet
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RNA Splicing, Cell Signaling and Response to Therapies
... regulated alternative splicing events across human solid ...recurrent alternative splicing switches in tumor samples reveals novel signatures of ...the RNA-Seq data ... Voir le document complet
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A Multi-Site Constraint Programming Model of Alternative Splicing Regulation
... Unité de recherche INRIA Lorraine LORIA, Technopôle de Nancy-Brabois - Campus scientifique 615, rue du Jardin Botanique - BP 101 - 54602 Villers-lès-Nancy Cedex France Unité de recherche[r] ... Voir le document complet
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De Novo Clustering of Long Reads by Gene from Transcriptomics Data
... read data generated via the Oxford Nanopore MinION, GridION or PromethION platforms, for transcriptome and full-length cDNA analysis (4, 9, 10, ...de novo assembly of a wide variety of species including ... Voir le document complet
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TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks
... expression data, two web tools were ...expression data in bar plot graphics, while the second tool generates pictures of tomato organs with arti- ficial background colors highlighting the expression levels ... Voir le document complet
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AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation.
... Each of the gene-transcript alignments is examined for the presence of a 3' dangling end on the transcript sequence. Only those alignments that show 3' dangling ends of length at least 8 bases are considered further. The ... Voir le document complet
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Reprogramming the Dynamin 2 mRNA by Spliceosome-mediated RNA Trans-splicing
... script from the exon 11 to the last ...sequence from exon 12 to exon 22 was modified by codon ...sequence from exon 1 to 11 including either exon 10 or 10 bis followed by Dnm2 optimized sequence ... Voir le document complet
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Dysregulation of cotranscriptional alternative splicing underlies CHARGE syndrome
... Figure S8. Fam172a physically interacts with Ago2 but not with Ago1. (A-B) Co-IP assays using whole cell extracts of COS7 cells (A; transfected with a Fam172a-expressing or empty vector) or of adult mouse olfactory ... Voir le document complet
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Domestication reduces alternative splicing expression variations in sorghum
... AS is recognised to be a “pivotal step between transcription and translation” [ 4 ]. It has been described as varying according to organ, according to developmental stages and even accord- ing to cell type [ 5 ]. AS ... Voir le document complet
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CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq
... Expression analysis pipeline CEL-Seq reads were processed into an expression matrix using a multistep, parallel computational pipeline within the Galaxy framework [6]. For CEL-Seq2, we developed a new pipeline as ... Voir le document complet
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Alternative RNA splicing in the endothelium mediated in part by Rbfox2 regulates the arterial response to low flow
... skipped-exon events, and those passing each filter. (B) Events were separated into those with increased or decreased inclusion, and then the sequences of the upstream and downstream 200 bp flanking regions ... Voir le document complet
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RNA-Seq profile of flavescence dorée phytoplasma in grapevine.
... The RNA-seq technology was successfully applied for the first time to analyse the FD global transcriptome profile during grapevine ...us from improving the genome annotation or from providing ... Voir le document complet
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The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B
... Western blots Total protein was isolated using standard RIPA lysis conditions (25 mM Tris-HCl, 150 mM NaCl, 1% NP-40, 1% deoxycholic acid, 0.1% SDS) and resolved by SDS polyacrylamide gel electrophoresis. Cell lysis was ... Voir le document complet
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Upstream ORF affects MYCN translation depending on exon 1b alternative splicing.
... Our results showed that, in transfected SH-EP neuroblast- oma cells, high MYCN dosage obtained with MYCN Δ1b mRNA translation induces a weak but significant antiap- optotic effect after serum deprivation that was not ... Voir le document complet
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Cross-kingdom patterns of alternative splicing and splice recognition
... Discussion Splice variation reveals mechanisms of splice site recognition The variation we observe in the CE fraction, the correspond- ence of this variation with average intron length, and the size constraints observed ... Voir le document complet
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CRAC: an integrated approach to the analysis of RNA-seq reads
... computation when analyzing RNA-seq. The combinatorial possibilities of aligning a read partly to two distinct regions on the same or different chromosomes [4] increase the likeliness of predicting FPs. It ... Voir le document complet
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