PXD006486-1

PXD006486 is an original dataset announced via ProteomeXchange.

Title	Identification of differentially expressed splice variants by the proteogenomic pipeline SPLICIFY
Description	Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, SPLICIFY, which is able to detect differentially expressed protein isoforms. SPLICIFY is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions. Proof of concept was obtained by applying SPLICIFY to RNA sequencing and mass spectrometry data obtained from colorectal cancer cell line SW480, before and after siRNA-mediated down-modulation of the splicing factors SF3B1 and SRSF1. These analyses revealed 2172 and 149 differentially expressed isoforms, respectively, with peptide confirmation upon knock-down of SF3B1 and SRSF1 compared to their controls. Splice variants identified included RAC1, OSBPL3, MKI67 and SYK.
HostingRepository	PRIDE
AnnounceDate	2017-07-28
AnnouncementXML	Submission_2017-07-28_12:32:55.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sander Piersma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-05-10 08:27:47	ID requested
⏵ 1	2017-07-28 12:32:56	announced
2	2024-10-22 04:39:48	announced	2024-10-22: Updated project metadata.

Komor MA, Pham TV, Hiemstra AC, Piersma SR, Bolijn AS, Schelfhorst T, Delis-van Diemen PM, Tijssen M, Sebra RP, Ashby M, Meijer GA, Jimenez CR, Fijneman RJA, Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify. Mol Cell Proteomics, 16(10):1850-1863(2017) [pubmed]

curator keyword: Technical, Biomedical

submitter keyword: Human, CRC, colorectal cancer, label-free, proteogenomics, splicing

Connie Ramona Jimenez
contact affiliation	OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
contact email	c.jimenez@vumc.nl
lab head
Sander Piersma
contact affiliation	OncoProteomics Laboratory, dept of Medical Oncology, VUmc Medical Center, Amsterdam, The Netherlands
contact email	s.piersma@vumc.nl
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/2017/07/PXD006486

PRIDE project URI

• PRIDE
  1. PXD006486
     1. Label: PRIDE project
     2. Name: Identification of differentially expressed splice variants by the proteogenomic pipeline SPLICIFY