PXD012565 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | INKA, an integrative analysis pipeline for inference of hyperactive phosphokinases in mass spectrometry-based phosphoproteomics data: CRC Organoids |
Description | CRC Organoid and corresponding PDX data are part of a larger project that includes proteomeXchange accessions PXD006616, PXD008032, and PXD009995. We present a computational pipeline called Integrative Inferred Kinase Activity (INKA) scoring that integrates the observed abundance of phosphopeptides derived from (i) kinases as a whole, (ii) their kinase activation loop segments, (iii) proteins deduced to be kinase substrates based on prior experimental knowledge of kinase-substrate relationships, and/or (iv) kinase substrates predicted by the sequence motif- and network-based NetworKIN algorithm. |
HostingRepository | PRIDE |
AnnounceDate | 2019-04-18 |
AnnouncementXML | Submission_2019-04-18_04:11:48.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 | phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-01-30 07:57:32 | ID requested | |
⏵ 1 | 2019-04-18 04:19:50 | announced | |
Publication List
Beekhof R, van Alphen C, Henneman AA, Knol JC, Pham TV, Rolfs F, Labots M, Henneberry E, Le Large TY, de Haas RR, Piersma SR, Vurchio V, Bertotti A, Trusolino L, Verheul HM, Jimenez CR, INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases. Mol Syst Biol, 15(4):e8250(2019) [pubmed] |
Keyword List
curator keyword: Technical, Biomedical |
submitter keyword: Human, CRC, phosphokinase ranking, label-free, single-shot, phosphoproteomics, PDX, Organoids |
Contact List
Connie Ramona Jimenez |
contact affiliation | Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD012565
- Label: PRIDE project
- Name: INKA, an integrative analysis pipeline for inference of hyperactive phosphokinases in mass spectrometry-based phosphoproteomics data: CRC Organoids