PXD022667 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Genoppi: an open-source software for robust and standardized integration of proteomic and genetic data |
Description | This 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. |
HostingRepository | PRIDE |
AnnounceDate | 2021-05-18 |
AnnouncementXML | Submission_2021-05-17_22:13:57.352.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Kasper Lage |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2020-11-23 08:04:31 | ID requested | |
1 | 2021-02-10 11:55:05 | announced | |
2 | 2021-05-17 22:11:34 | announced | 2021-05-18: Updated project metadata. |
⏵ 3 | 2021-05-17 22:13:58 | announced | 2021-05-18: 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 affiliation | Massachusetts General Hospital, USA |
contact email | lage.kasper@mgh.harvard.edu |
lab head | |
Kasper Lage |
contact affiliation | Massachusetts General Hospital |
contact email | klagelab@gmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD022667
- Label: PRIDE project
- Name: Genoppi: an open-source software for robust and standardized integration of proteomic and genetic data