TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes
Autor: | Sadashivam Abinaya, Kshitish K. Acharya, Darshan S. Chandrashekar, Govindkumar Balagannavar, Neelima Chitturi, Vasan S Srini |
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Rok vydání: | 2013 |
Předmět: |
Gene isoform
Quality Control Microarray Alternatively spliced Biology Transcript isoforms Mice Affymetrix Gene expression Databases Genetic Genetics RNA Isoforms Microarray databases Animals Humans mRNA isoforms Oligonucleotide Array Sequence Analysis Azoospermia Internet Microarray analysis techniques Gene Expression Profiling Alternative splicing Computational Biology Reproducibility of Results Rats Gene expression profiling Alternative Splicing DNA microarray Transcriptome Software Biotechnology |
Zdroj: | BMC Genomics |
ISSN: | 1471-2164 |
Popis: | Background Standard 3′ Affymetrix gene expression arrays have contributed a significantly higher volume of existing gene expression data than other microarray platforms. These arrays were designed to identify differentially expressed genes, but not their alternatively spliced transcript forms. No resource can currently identify expression pattern of specific mRNA forms using these microarray data, even though it is possible to do this. Results We report 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. The tool has been experimentally validated for mRNAs transcribed or not-detected in a human disease condition (non-obstructive azoospermia, a male infertility condition). About 4000 gene expression datasets were downloaded from a public repository. ‘Good probes’ with complete coverage and identity to latest reference transcript sequences were first identified. Using them, ‘Transcript specific probe-clusters’ were derived for each platform and used to identify expression status of possible transcripts. The web server can lead the user to datasets corresponding to specific tissues, conditions via identifiers of the microarray studies or hybridizations, keywords, official gene symbols or reference transcript identifiers. It can identify, in the tissues and conditions of interest, about 40% of known transcripts as ‘transcribed’, ‘not-detected’ or ‘differentially regulated’. Corresponding additional information for probes, genes, transcripts and proteins can be viewed too. We identified the expression of transcripts in a specific clinical condition and validated a few of these transcripts by experiments (using reverse transcription followed by polymerase chain reaction). The experimental observations indicated higher agreements with the web server results, than contradictions. The tool is accessible at http://resource.ibab.ac.in/TIPMaP. Conclusion The newly developed online tool forms a reliable means for identification of alternatively spliced transcript-isoforms that may be differentially expressed in various tissues, cell types or physiological conditions. Thus, by making better use of existing data, TIPMaP avoids the dependence on precious tissue-samples, in experiments with a goal to establish expression profiles of alternative splice forms – at least in some cases. |
Databáze: | OpenAIRE |
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