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A powerful statistical approach for large-scale differential transcription analysis.

ABSTRACT: Next generation sequencing (NGS) is increasingly being used for transcriptome-wide analysis of differential gene expression. The NGS data are multidimensional count data. Therefore, most of the statistical methods developed well for microarray data analysis are not applicable to transcriptomic data. For this reason, a variety of new statistical methods based on count data of transcript reads have been correspondingly proposed. But due to high cost and limitation of biological resources, current NGS data are still generated from a few replicate libraries. Some of these existing methods do not always have desirable performances on count data. We here developed a very powerful and robust statistical method based on beta and binomial distributions. Our method (mBeta t-test) is specifically applicable to sequence count data from small samples. Both simulated and real transcriptomic data showed mBeta t-test significantly outperformed the existing top statistical methods chosen in all 12 given scenarios and performed with high efficiency and high stability. The differentially expressed genes found by our method from real transcriptomic data were validated by qPCR experiments. Our method shows high power in finding truly differential expression, conservatively estimating FDR and high stability in RNA sequence count data derived from small samples. Our method can also be extended to genome-wide detection of differential splicing events.

SUBMITTER: Tan YD

PROVIDER: S-EPMC4404056 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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A powerful statistical approach for large-scale differential transcription analysis.

Tan Yuan-De YD Chandler Anita M AM Chaudhury Arindam A Neilson Joel R JR

PloS one 20150420 4

Next generation sequencing (NGS) is increasingly being used for transcriptome-wide analysis of differential gene expression. The NGS data are multidimensional count data. Therefore, most of the statistical methods developed well for microarray data analysis are not applicable to transcriptomic data. For this reason, a variety of new statistical methods based on count data of transcript reads have been correspondingly proposed. But due to high cost and limitation of biological resources, current ...[more]

PMID: 25894390

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Project description:BackgroundSystems biology aims to analyse regulation mechanisms into the cell. By mapping interactions observed in different situations, differential network analysis has shown its power to reveal specific cellular responses or specific dysfunctional regulations. In this work, we propose to explore on a large scale the role of natural anti-sense transcription on gene regulation mechanisms, and we focus our study on apple (Malus domestica) in the context of fruit ripening in cold storage.ResultsWe present a differential functional analysis of the sense and anti-sense transcriptomic data that reveals functional terms linked to the ripening process. To develop our differential network analysis, we introduce our inference method of an Extended Core Network; this method is inspired by C3NET, but extends the notion of significant interactions. By comparing two extended core networks, one inferred with sense data and the other one inferred with sense and anti-sense data, our differential analysis is first performed on a local view and reveals AS-impacted genes, genes that have important interactions impacted by anti-sense transcription. The motifs surrounding AS-impacted genes gather transcripts with functions mostly consistent with the biological context of the data used and the method allows us to identify new actors involved in ripening and cold acclimation pathways and to decipher their interactions. Then from a more global view, we compute minimal sub-networks that connect the AS-impacted genes using Steiner trees. Those Steiner trees allow us to study the rewiring of the AS-impacted genes in the network with anti-sense actors.ConclusionAnti-sense transcription is usually ignored in transcriptomic studies. The large-scale differential analysis of apple data that we propose reveals that anti-sense regulation may have an important impact in several cellular stress response mechanisms. Our data mining process enables to highlight specific interactions that deserve further experimental investigations.

Dataset Information

A powerful statistical approach for large-scale differential transcription analysis.

Publications

A powerful statistical approach for large-scale differential transcription analysis.

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