PXD010192

PXD010192 is an original dataset announced via ProteomeXchange.

Title	Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury
Description	Spinal cord injury (SCI) is a devastating neurological condition for which there are currently no effective treatment options to restore function. A major obstacle to the development of new therapies is our fragmentary understanding of the coordinated pathophysiological processeses triggered by damage to the human spinal cord. An additional challenge to translation of preclinical therapies is the reliance of clinical trials on standardized neurological assessments to enrol and stratify patients, rather than objective injury biomarkers. Here, we describe a systems biology approach to integrate decades of small-scale experiments with unbiased, genome-wide gene expression from the human spinal cord, revealing a gene regulatory network signature of the pathophysiological response to SCI. Our integrative analyses converge on an evolutionarily conserved gene subnetwork enriched for genes associated with the response to SCI by small-scale experiments, and whose expression is upregulated in a severity-dependent manner following injury and downregulated in functional recovery. We validate the severity-dependent upregulation of this subnetwork in prospective transcriptomic and proteomic studies. Our analysis provides a systems-level view of the coordinated molecular processes activated in response to SCI. Further, our results nominate quantitative biomarkers of injury severity and functional recovery, with the potential to facilitate development and translation of novel therapies.
HostingRepository	PRIDE
AnnounceDate	2018-09-25
AnnouncementXML	Submission_2019-02-12_08:26:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jenny Moon
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	No PTMs are included in the dataset
Instrument	Bruker Daltonics instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2018-06-22 02:40:35	ID requested
1	2018-09-25 08:45:25	announced
⏵ 2	2019-02-12 08:26:49	announced	Updated publication reference for PubMed record(s): 30277459.

Squair JW, Tigchelaar S, Moon KM, Liu J, Tetzlaff W, Kwon BK, Krassioukov AV, West CR, Foster LJ, Skinnider MA, Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury. Elife, 7():(2018) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: rat, spinal cord injury

Leonard J. Foster
contact affiliation	Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC, Canada
contact email	foster@msl.ubc.ca
lab head
Jenny Moon
contact affiliation	University of British Columbia
contact email	kyungmee@mail.ubc.ca
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/2018/09/PXD010192

PRIDE project URI

• PRIDE
  1. PXD010192
     1. Label: PRIDE project
     2. Name: Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury