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dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes
- Source :
- BMC Bioinformatics, BMC Bioinformatics, Vol 13, Iss 1, p 271 (2012)
- Publication Year :
- 2012
- Publisher :
- BioMed Central, 2012.
-
Abstract
- Background Dysregulation of imprinted genes, which are expressed in a parent-of-origin-specific manner, plays an important role in various human diseases, such as cancer and behavioral disorder. To date, however, fewer than 100 imprinted genes have been identified in the human genome. The recent availability of high-throughput technology makes it possible to have large-scale prediction of imprinted genes. Here we propose a Bayesian model (dsPIG) to predict imprinted genes on the basis of allelic expression observed in mRNA-Seq data of independent human tissues. Results Our model (dsPIG) was capable of identifying imprinted genes with high sensitivity and specificity and a low false discovery rate when the number of sequenced tissue samples was fairly large, according to simulations. By applying dsPIG to the mRNA-Seq data, we predicted 94 imprinted genes in 20 cerebellum samples and 57 imprinted genes in 9 diverse tissue samples with expected low false discovery rates. We also assessed dsPIG using previously validated imprinted and non-imprinted genes. With simulations, we further analyzed how imbalanced allelic expression of non-imprinted genes or different minor allele frequencies affected the predictions of dsPIG. Interestingly, we found that, among biallelically expressed genes, at least 18 genes expressed significantly more transcripts from one allele than the other among different individuals and tissues. Conclusion With the prevalence of the mRNA-Seq technology, dsPIG has become a useful tool for analysis of allelic expression and large-scale prediction of imprinted genes. For ease of use, we have set up a web service and also provided an R package for dsPIG at http://www.shoudanliang.com/dsPIG/.
- Subjects :
- Sequence analysis
Gene Expression
Biology
Allelic Imbalance
lcsh:Computer applications to medicine. Medical informatics
Biochemistry
Genome
Polymorphism, Single Nucleotide
Genomic Imprinting
Gene Frequency
Structural Biology
Humans
RNA, Messenger
Molecular Biology
Allele frequency
Gene
lcsh:QH301-705.5
Alleles
Analysis of allelic expression
Genetics
mRNA-Seq
Base Sequence
Models, Genetic
Genome, Human
Applied Mathematics
Gene Expression Profiling
High-Throughput Nucleotide Sequencing
Bayes Theorem
Sequence Analysis, DNA
Computer Science Applications
Minor allele frequency
Gene expression profiling
Prediction of imprinted genes
lcsh:Biology (General)
Bayesian model
Transcriptome deep sequencing
lcsh:R858-859.7
DNA microarray
Genomic imprinting
Transcriptome
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 14712105
- Volume :
- 13
- Database :
- OpenAIRE
- Journal :
- BMC Bioinformatics
- Accession number :
- edsair.doi.dedup.....33208861aea770001f2b8f49af50fdc8