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PXD006486

PXD006486 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIdentification of differentially expressed splice variants by the proteogenomic pipeline SPLICIFY
DescriptionProteogenomics, 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:39:39.722.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSander Piersma
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02017-05-10 08:27:47ID requested
12017-07-28 12:32:56announced
22024-10-22 04:39:48announced2024-10-22: Updated project metadata.
Publication List
10.1074/mcp.TIR117.000056;
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]
Keyword List
curator keyword: Technical, Biomedical
submitter keyword: Human, proteogenomics, splicing, CRC, label-free, colorectal cancer
Contact List
Connie Ramona Jimenez
contact affiliationOncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
contact emailc.jimenez@vumc.nl
lab head
Sander Piersma
contact affiliationOncoProteomics Laboratory, dept of Medical Oncology, VUmc Medical Center, Amsterdam, The Netherlands
contact emails.piersma@vumc.nl
dataset submitter
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Dataset FTP location
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PRIDE project URI
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