⮝ Full datasets listing

PXD022667

PXD022667 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleGenoppi: an open-source software for robust and standardized integration of proteomic and genetic data
DescriptionThis submission contains human protein interaction datasets of four proteins (BCL2, TDP-43, MDM2, PTEN) across three cancer cell lines (G401, T47D, A375) and one iPSC-derived neuronal cell line (glutamatergic patterned induced neuron, GPiN). The data were generated to demonstrate the utility of Genoppi (lagelab.org/genoppi), an open-source computational tool that enables integration of quantitative proteomic results with genetic data. Our analyses show a general pattern of both cell-type-independent and cell-type-specific interactions for the tested proteins. In particular, our results suggest that the neuron-specific interactions of BCL2 and TDP-43 are mediating their genetic involvement in amyotrophic lateral sclerosis.
HostingRepositoryPRIDE
AnnounceDate2021-05-18
AnnouncementXMLSubmission_2021-05-17_22:13:57.352.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterKasper Lage
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListphosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-11-23 08:04:31ID requested
12021-02-10 11:55:05announced
22021-05-17 22:11:34announced2021-05-18: Updated project metadata.
32021-05-17 22:13:58announced2021-05-18: Updated project metadata.
Publication List
Pintacuda G, Lassen FH, Hsu YH, Kim A, Mart, í, n JM, Malolepsza E, Lim JK, Fornelos N, Eggan KC, Lage K, Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data. Nat Commun, 12(1):2580(2021) [pubmed]
Keyword List
submitter keyword: neuron and cancer cells, PTEN, BCL2, label-free quantification, MDM2, protein-protein interactions,endogenous IP-MS, TDP-43
Contact List
Kasper Lage
contact affiliationMassachusetts General Hospital, USA
contact emaillage.kasper@mgh.harvard.edu
lab head
Kasper Lage
contact affiliationMassachusetts General Hospital
contact emailklagelab@gmail.com
dataset submitter
Full Dataset Link List
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/2021/02/PXD022667
PRIDE project URI
Repository Record List
[ + ]