PT  - JOURNAL ARTICLE
AU  - Surojit Biswas
AU  - Konstantin Kerner
AU  - Paulo José Pereira Lima Teixeira
AU  - Jeffery L. Dangl
AU  - Vladimir Jojic
AU  - Philip A. Wigge
TI  - Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes
AID  - 10.1101/060111
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 060111
4099  - http://biorxiv.org/content/early/2016/10/11/060111.short
4100  - http://biorxiv.org/content/early/2016/10/11/060111.full
AB  - 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.