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RAX2: a genome-wide detection method of condition-associated transcription variation.

ABSTRACT: Most mammalian genes have mRNA variants due to alternative promoter usage, alternative splicing, and alternative cleavage and polyadenylation. Expression of alternative RNA isoforms has been found to be associated with tumorigenesis, proliferation and differentiation. Detection of condition-associated transcription variation requires association methods. Traditional association methods such as Pearson chi-square test and Fisher Exact test are single test methods and do not work on count data with replicates. Although the Cochran Mantel Haenszel (CMH) approach can handle replicated count data, our simulations showed that multiple CMH tests still had very low power. To identify condition-associated variation of transcription, we here proposed a ranking analysis of chi-squares (RAX2) for large-scale association analysis. RAX2 is a nonparametric method and has accurate and conservative estimation of FDR profile. Simulations demonstrated that RAX2 performs well in finding condition-associated transcription variants. We applied RAX2 to primary T-cell transcriptomic data and identified 1610 (16.3%) tags associated in transcription with immune stimulation at FDR < 0.05. Most of these tags also had differential expression. Analysis of two and three tags within genes revealed that under immune stimulation short RNA isoforms were preferably used.

SUBMITTER: Tan YD

PROVIDER: S-EPMC4551904 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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RAX2: a genome-wide detection method of condition-associated transcription variation.

Tan Yuan-De YD Deng Jixin J Neilson Joel R JR

Nucleic acids research 20150507 15

Most mammalian genes have mRNA variants due to alternative promoter usage, alternative splicing, and alternative cleavage and polyadenylation. Expression of alternative RNA isoforms has been found to be associated with tumorigenesis, proliferation and differentiation. Detection of condition-associated transcription variation requires association methods. Traditional association methods such as Pearson chi-square test and Fisher Exact test are single test methods and do not work on count data wit ...[more]

PMID: 25953852

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Dataset Information

RAX2: a genome-wide detection method of condition-associated transcription variation.

Publications

RAX2: a genome-wide detection method of condition-associated transcription variation.

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