RT Journal Article
SR Electronic
T1 Tradict enables high fidelity reconstruction of the eukaryotic transcriptome from 100 marker genes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 060111
DO 10.1101/060111
A1 Surojit Biswas
A1 Konstantin Kerner
A1 Paulo José Pereira Lima Teixeira
A1 Jeffery L Dangl
A1 Vladimir Jojic
A1 Philip A. Wigge
YR 2016
UL http://biorxiv.org/content/early/2016/06/21/060111.abstract
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, we reasoned it might be accurately represented by a subset of transcript abundances. We develop a method, Tradict (transcriptome predict), capable of learning and using the expression measurements of a small subset of 100 marker genes to reconstruct entire transcriptomes. By analyzing over 23,000 publicly available RNA-Seq datasets, we show that Tradict is robust to noise and accurate, especially for predicting the expression of a comprehensive, but interpretable list of transcriptional programs that represent the major biological processes and cellular pathways. Coupled with targeted RNA sequencing, Tradict may therefore enable simultaneous transcriptome-wide screening and mechanistic investigation at large scales. Thus, whether for performing forward genetic, chemogenomic, or agricultural screens or for profiling single-cells, Tradict promises to help accelerate genetic dissection and drug discovery.