PXD002371

PXD002371 is an original dataset announced via ProteomeXchange.

Title	Environmental interactions and epistasis are revealed in the proteomic responses to complex stimuli
Description	Ultimately, the genotype of a cell and its interaction with the environment determine the cell’s biochemical state. While the cell’s response to a single stimulus has been studied extensively, a conceptual framework to model the effect of multiple environmental stimuli applied concurrently is not as well developed. In this study, we developed the concepts of environmental interactions and epistasis to explain the responses of the S. cerevisiae proteome to simultaneous environmental stimuli. We hypothesize that, as an abstraction, environmental stimuli can be treated as analogous to genetic elements. This would allow modeling of the effects of multiple stimuli using the concepts and tools developed for studying gene interactions. Mirroring gene interactions, our results show that environmental interactions play a critical role in determining the state of the proteome. We show that individual and complex environmental stimuli behave similarly to genetic elements in regulating the cellular responses to stimuli, including the phenomena of dominance and suppression. Interestingly, we observed that the effect of a stimulus on a protein is dominant over other stimuli if the response to the stimulus involves the protein. Using publicly available transcriptomic data, we find that environmental interactions and epistasis regulate transcriptomic responses as well.
HostingRepository	PRIDE
AnnounceDate	2019-02-12
AnnouncementXML	Submission_2019-02-12_07:53:13.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andrew Link
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	methylthiolated residue; monohydroxylated residue; deamidated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-15 01:57:24	ID requested
1	2015-07-20 05:43:58	announced
⏵ 2	2019-02-12 07:53:15	announced	Updated publication reference for PubMed record(s): 26247773.

Samir P, Rahul, Slaughter JC, Link AJ, Environmental Interactions and Epistasis Are Revealed in the Proteomic Responses to Complex Stimuli. PLoS One, 10(8):e0134099(2015) [pubmed]

curator keyword: Biological

submitter keyword: Yeast, Saccharomyces cerevisiae, iTRAQ, MudPIT, environmental interaction, environmental epistasis

Andrew Link
contact affiliation	Dept of Pathology, Microbiology and Immunology Vanderbilt University School of Medicine
contact email	andrew.link@vanderbilt.edu
lab head
Andrew Link
contact affiliation	Vanderbilt University School of Medicine
contact email	andrew.link@vanderbilt.edu
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/2015/07/PXD002371

PRIDE project URI

• PRIDE
  1. PXD002371
     1. Label: PRIDE project
     2. Name: Environmental interactions and epistasis are revealed in the proteomic responses to complex stimuli