Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data

Rambaldi, Davide; Felice, Barbara; Praz, Viviane; Bücher, Philipp; Cittaro, Davide; Guffanti, Alessandro

doi:10.1186/1471-2105-8-s1-s17

Cited by 9 publications

(8 citation statements)

References 14 publications

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“… 21 All these corroborate that alternative splicing exerts significant roles in the regulation of cellular differentiation and apoptosis. 22 Additionally, multiple variants of the splice factors including Eftud2 and Snrpd2 have been discovered in the inflammatory breast cancer cell lines, 23 suggesting their potential roles in the inflammation. In our present study, up-regulated Eftud2 and Snrpd2 were both enriched in RNA splicing BP, consistent with the functional enrichment analysis in fatal familial insomnia in brain tissues, 24 further supporting the involvement of the two genes in this process.…”

Section: Discussionmentioning

confidence: 99%

Gene markers of fracture healing in early stage and the regulatory mechanism during the process using microarray analysis

Wang

Tan

et al. 2016

Acta Orthopaedica et Traumatologica Turcica

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BackgroundThe aim of this study was to explore crucial markers and uncover the regulatory mechanisms of fracture healing in the early stage.MethodsGene expression profile of GSE45156 was downloaded, in which 3 fractured samples and 3 unfractured samples were used in our present study. Based on the threshold value, differentially expressed genes (DEGs) were selected between two kinds of samples using limma package in R. Enrichment analysis of these DEGs was performed by DAVID software. Furthermore, protein-protein interaction (PPI) network was established integrating information in STRING database, and visualized by Cytoscape software.ResultsWe identified a set of 960 DEGs including 509 up-regulated and 451 downregulated genes. Biological processes involving RNA splicing and cell cycle were significantly enriched for the up-regulated genes such as Snrpd2, Eftud2, Plk1 and Bub1b, whereas skeletal system development and bone development processes were predominant for down-regulated genes like Ubc. In the constructed PPI network, all the five genes were the predominant nodes, of which Snrpd2 was linked to Eftud2, while Bub1b was to interact with Plk1.ConclusionFive candidate genes crucial for indicating the process of fracture in early stage were identified. Eftud2, Snrpd2, Bub1b and Plk1 might function through the involvement of cell-cycle-related BP, while Ubc might influence the protein degradation during bone development. However, more experimental validations are needed to confirm these results.

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Section: Discussionmentioning

confidence: 99%

Gene markers of fracture healing in early stage and the regulatory mechanism during the process using microarray analysis

Wang

Tan

et al. 2016

Acta Orthopaedica et Traumatologica Turcica

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“…MAASE [109] is also specifically designed to apply in splicing microarray experiments. In contrast, Splicy [115] provide the web-based tool to predict possible alternative splicing events from Affymetrix probe set inputs. ASTALAVISTA [116] provides alternative splicing prediction for transcriptome data from GENCODE, REFSEQ, and ENSEMBL as well as from custom gene datasets.…”

Section: Alternative Splicing-related Bioinformatics Resourcesmentioning

confidence: 99%

Alternative Splicing for Diseases, Cancers, Drugs, and Databases

Tang

Lee

Hou

et al. 2013

The Scientific World Journal

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Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.

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“…The CleanEx Affymetrix (http://www.affymetrix.com) mapping files are now also accessible by an external Affymetrix probes viewer called Splicy (http://host10.bioinfo3.ifom-ieo-campus.it/splicy/) (6). …”

Section: Introductionmentioning

confidence: 99%

CleanEx: new data extraction and merging tools based on MeSH term annotation

Praz

Bücher

2009

Nucleic Acids Research

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The CleanEx expression database (http://www.cleanex.isb-sib.ch) provides access to public gene expression data via unique gene names as well as via experiments biomedical characteristics. To reach this, a dual annotation of both sequences and experiments has been generated. First, the system links official gene symbols to any kind of sequences used for gene expression measurements (cDNA, Affymetrix, oligonucleotide arrays, SAGE or MPSS tags, Expressed Sequence Tags or other mRNA sequences, etc.). For the biomedical annotation, we re-annotate each experiment from the CleanEx database with the MeSH (Medical Subject Headings) terms, primarily used by NLM (National Library of Medicine) for indexing articles for the MEDLINE/PubMED database. This annotation allows a fast and easy retrieval of expression data with common biological or medical features. The numerical data can then be exported as matrix-like tab-delimited text files. Data can be extracted from either one dataset or from heterogeneous datasets.

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Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data

Cited by 9 publications

References 14 publications

Gene markers of fracture healing in early stage and the regulatory mechanism during the process using microarray analysis

Gene markers of fracture healing in early stage and the regulatory mechanism during the process using microarray analysis

Alternative Splicing for Diseases, Cancers, Drugs, and Databases

CleanEx: new data extraction and merging tools based on MeSH term annotation

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