Alternative splicing identification software tools | Gene expression microarray data analysis
The analysis of differential splicing (DS) is crucial for understanding physiological processes in cells and organs. In particular, aberrant transcripts are known to be involved in various diseases including cancer. A widely used technique for studying DS are exon arrays.
An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichment and more).
An R function that for a given set of exon arrays corrects for the observed bias and improves the detection of alternative splicing. COSIE adjusts splicing indices for exons, especially for those that belong to differentially expressed genes. For this adjustment, COSIE uses parameters that are specific for each probeset which were trained from a large number of published exon arrays. The downside of this approach is that such parameters cannot be estimated for all probesets on the microarray.
An R package that is designed to preprocess, analyze and visualize Affymetrix GeneChip exon array data. MEAP contains modules for data pre-processing, differential expression analysis, and visualization. Data pre-processing uses a novel background estimation model (PM-BayesBG) and is followed by collective quantile normalization and multi-dimensional expression summarization based on user defined data type (probeset, exon, spliced variant or gene). Differential analysis enables finding biologically interesting targets. The workflow also includes web-based visualization for alternatively spliced events. MEAP produces reliable expression values at exon, alternatively spliced variant and gene levels, which allows generating novel experimentally testable predictions.
Disaggregates the signal at 'multi-match' probes. When applied to Gene arrays, MMBGX removes the upward bias of gene-level expression estimates. When applied to Exon arrays, it can further disaggregate the signal between alternative transcripts of the same gene, providing expression estimates of individual splice variants.
A robust methodology for detection of alternative exon usage (AEU) events using global transcriptome data, yielding results with limited requirement for visual inspection and a high true positive rate. Our meta-analysis indicates that RNA-seq protocols do not provide sufficient quantification of much of the transcriptome (‘read coverage’), which limits alternative splicing analysis of RNA-seq data to only the highest abundance transcripts.
Searches and analyzes alternative splicing (AS) events using Human Transcriptome Array 2.0 (HTA 2.0). EventPointer uses a linear model that broadens its application from plain case-control studies to complex experimental designs. It retrieves a list of all the detected events indicating: 1) the type of event; (2) its fold change and its statistical significance; and (3) the potential protein domains affected by the AS events and the statistical significance of the possible enrichment.
Provides methods for gene and transcript expression summarisation and uncertainty propagation methods for the downstream analysis. puma supports a wide range of quantitative expression analysis of microarray at both gene and isoform level. It enables reliable estimation of isoform expression from Exon array data. This tool is able to take into account the within-chip measurement error and across-chip technical and biological variance.
A method for detecting differential alternative splicing in exon array data. FIRMA has been developed for Affymetrix exon arrays, but could in principle other exon arrays, tiling arrays or splice junction arrays. R code implementing FIRMA is contributed to the package aroma.affymetrix.
A statistical method to detect alternative splicing from expression data. Since ANOSVA requires no transcript information, it can be applied when the level of annotation is poor. When validated against spiked clone data, it generated no false positives and few false negatives.
An entropy-based measure for splicing prediction. ARH is based on a simple, robust model based on the exon expression ratios with respect to two experimental conditions. A deviation in exons leads to a dominating effect on the entropy and a high ARH value. ARH takes into account probe affinities and variable exon mRNA abundances by computing exon expression ratios between samples.
Serve as a starting point for the community to perform additional experiments, including high-throughput methods such as oligonucleotide microarrays studies, to identify functional alternative splicing (AS) events in plants. ASIP uses the characteristics of AS legumes, on the basis of expressed sequence tag (EST) alignments to different genome sequences.
A web server for expression profiling of alternatively spliced transcripts using microarray data sets from 31 standard 3' Affymetrix arrays for human, mouse and rat species. TIPMaP has been experimentally validated for mRNAs transcribed or not-detected in a human disease condition (non-obstructive azoospermia, a male infertility condition).
Provides a probe-level analysis of gene expression microarray data. Rmodel is an open-source package which allows users to segment a microarray probe set to identify novel processing events. The software tests all possible segmentations to determine the sequence boundaries of transcribed regions.
Allows to query Evidence Viewer Database (EVDB). SpliceMiner maps probes to splice variants. The database contains non-redundant compendium of splice variant data for human genes. It can be searched by gene symbol, genomic coordinates, or probe sequence. The tool provides a way for improving the accuracy of microarray results through inclusion of splice variant and exon composition data. It can be integrated into a variety of microarray pipelines.
A Java-based freeware to process, filtrate and visualize exon array data with an analysis pipeline. This tool implements the most commonly used probeset summarization methods as well as AS-orientated filtration algorithms, e.g. MIDAS and PAC, for the detection of alternative splicing events. The simplicity, flexibility and brevity of easyExon make it a valuable tool for AS event identification in genomic research.
An improved regression model to select alternatively spliced genes and exons from exon array data. Both simulation and real data analysis indicate that REMAS has convincing capability in identification of AS events.
A web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1) data normalization, (2) statistical analysis based on two-way ANOVA, (3) finding transcripts with significantly different splice patterns, (4) efficient visualization based on heatmaps and barplots, and (5) meta-analysis to detect exon level biomarkers.
Recognizes differential expression in Affymetrix gene expression microarray studies. PECA calculates the probe-level expression changes using the ordinary or modified t-statistic. This tool can also be useful in proteomic studies. It uses a probe-level expression change averaging (PECA) method to detect differential expression.
A computational pipeline to detect differential splicing events from the Affymetrix exon junction array data. For each alternative splicing event, MADS+ evaluates the signals of probes targeting competing transcript isoforms to identify exons or splice sites with different levels of transcript inclusion between two sample groups. MADS+ is used routinely in our analysis of Affymetrix exon junction arrays and has a high accuracy in detecting differential splicing events.