Universität zu Köln

Biswas, Surojit, Kerner, Konstantin, Teixeira, Paulo Jose Pereira Lima, Dangl, Jeffery L., Jojic, Vladimir and Wigge, Philip A. (2017). Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes. Nat. Commun., 8. LONDON: NATURE PUBLISHING GROUP. ISSN 2041-1723

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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 develop 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 data sets, 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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Biswas, Surojit UNSPECIFIED UNSPECIFIED UNSPECIFIED Kerner, Konstantin UNSPECIFIED UNSPECIFIED UNSPECIFIED Teixeira, Paulo Jose Pereira Lima UNSPECIFIED UNSPECIFIED UNSPECIFIED Dangl, Jeffery L. UNSPECIFIED UNSPECIFIED UNSPECIFIED Jojic, Vladimir UNSPECIFIED UNSPECIFIED UNSPECIFIED Wigge, Philip A. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-231311
DOI:	10.1038/ncomms15309
Journal or Publication Title:	Nat. Commun.
Volume:	8
Date:	2017
Publisher:	NATURE PUBLISHING GROUP
Place of Publication:	LONDON
ISSN:	2041-1723
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language NETWORKS; QUANTIFICATION; ALGORITHMS; PURSUIT Multiple languages Multidisciplinary Sciences Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/23131