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PXD041269 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleTapioca – A Novel Platform for Prediction Of Protein-Protein Interaction Dynamics Identifies NUCKS1 as a Broad-Spectrum Herpesvirus Proviral Factor
DescriptionUnderstanding protein-protein interaction (PPI) network dynamics is key to understanding nominal and perturbed cell states. Here, we develop a new machine learning framework called Tapioca that allows for the study of PPIs in dynamics contexts at a global scale in ex/in vivo conditions. Furthermore, we optimized the thermal denaturation and lysis conditions used in the thermal proximity coaggregation (TPCA) methodology, one of the types of data Tapioca can use to make predictions. Using this optimized protocol and Tapioca, we investigated the temporal dynamics of reactivation from latency of the oncogenic gammaherpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV), identifying the host protein NUCKS1 as a factor promoting KSHV genome replication during lytic infection. Integrating this dataset with published TPCA datasets from the alphaherpesvirus herpes simplex virus type-1 (HSV-1) and the betaherpesvirus human cytomegalovirus (HCMV), we determined NUCKS1 to have a proviral role across all three herpesvirus subfamilies.
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterMatthew Tyl
SpeciesList scientific name: Human herpesvirus 8 strain GK18; NCBI TaxID: 868565; scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-04-01 13:21:24ID requested
12023-12-02 23:42:22announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: TPCA, IP, PRM, KSHV
Contact List
Ileana Cristea
contact affiliationDepartment of Molecular Biology, Princeton University
contact emailicristea@princeton.edu
lab head
Matthew Tyl
contact affiliationDepartment of Molecular Biology, Princeton University
contact emailmtyl@princeton.edu
dataset submitter
Full Dataset Link List
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