PXD024258

PXD024258 is an original dataset announced via ProteomeXchange.

Title	iTARGEX analysis of yeast deletome reveals novel regulators of transcriptional buffering in S phase and protein turnover
Description	Integrating omics data with quantification of biological traits provides unparalleled opportunities for discovery of genetic regulators by in silico inference. However, current approaches to analyze genetic-perturbation screens are limited by their reliance on annotation libraries for prioritization of hits and subsequent targeted experimentation. Here, we present iTARGEX (identification of Trait-Associated Regulatory Genes via mixture regression using EXpectation maximization), an association framework with no requirement of a priori knowledge of gene function. After creating this tool, we used it to test associations between gene expression profiles and two biological traits in single-gene-deleted budding yeast mutants, including transcription homeostasis during S phase and global protein turnover. For each trait, we discovered novel regulators without prior functional annotations. The functional effects of the novel candidates were then validated experimentally, providing solid evidence for their roles in the respective traits. Hence, we conclude that iTARGEX can reliably identify novel factors involved in given biological traits. As such, it is capable of converting genome-wide observations into causal gene function predictions. Further application of iTARGEX in other contexts is expected to facilitate the discovery of new regulators and provide observations for novel mechanistic hypotheses regarding different biological traits and phenotypes.
HostingRepository	PRIDE
AnnounceDate	2021-09-10
AnnouncementXML	Submission_2021-09-10_00:36:51.387.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cheng-Fu Kao
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-19 07:38:01	ID requested
⏵ 1	2021-09-10 00:36:52	announced

Huang JH, Liao YR, Lin TC, Tsai CH, Lai WY, Chou YK, Leu JY, Tsai HK, Kao CF, iTARGEX analysis of yeast deletome reveals novel regulators of transcriptional buffering in S phase and protein turnover. Nucleic Acids Res, 49(13):7318-7329(2021) [pubmed]

submitter keyword: iTARGEX, Transcriptional buffering, Protein turnover

Cheng-Fu Kao
contact affiliation	Institution of Cellular and Organismic Biology Academia Sinica
contact email	ckao@gate.sinica.edu.tw
lab head
Cheng-Fu Kao
contact affiliation	Institute of Cellular and Organismic Biology, Academia Sinica.
contact email	ckao@gate.sinica.edu.tw
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD024258

PRIDE project URI

• PRIDE
  1. PXD024258
     1. Label: PRIDE project
     2. Name: iTARGEX analysis of yeast deletome reveals novel regulators of transcriptional buffering in S phase and protein turnover