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bioRxiv · 10.1101/060111

Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes

Surojit Biswas·Konstantin Kerner·Paulo Jose Pereira Lima Teixeira·Jeffery L Dangl·Vladimir Jojic·Philip A. Wigge
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Abstract

Transcript levels are a critical determinant of the proteome and hence cellular function. Because the transcriptome is an outcome of the interactions between genes and their products, it may be accurately represented by a subset of transcript abundances. We developed a method, Tradict (transcriptome predict), capable of learning and using the expression measurements of a small subset of 100 marker genes to predict transcriptome-wide gene abundances and the expression of a comprehensive, but interpretable list of transcriptional programs that represent the major biological processes and pathways of the cell. By analyzing over 23,000 publicly available RNA-Seq datasets, we show that Tradict is robust to noise and accurate. Coupled with targeted RNA sequencing, Tradict may therefore enable simultaneous transcriptome-wide screening and mechanistic investigation at large scales.

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Surojit Biswas, Konstantin Kerner, Paulo Jose Pereira Lima Teixeira, Jeffery L Dangl, Vladimir Jojic, Philip A. Wigge. 2016-06-21. Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes. https://doi.org/10.1101/060111

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