PXD037866 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | PRM of eGFP and mCherry in human cells |
Description | We leverage existing state-of-the-art transcriptomics and proteomics datasets from the GTEx project and the Human Protein Atlas to compute the protein-to-mRNA ratios of 36 human tissues. Using this as a proxy of translational efficiency, we build a machine learning model that identifies codons enriched or depleted in specific tissues. In particular, we detect two clusters of tissues with an opposite pattern of codon preferences. We then use the identified patterns for the development of CUSTOM (https://custom.crg.eu), a codon optimizer algorithm which suggests a synonymous codon design in order to optimize protein production in a tissue-specific manner. In a human cell model, we provide evidence that codon optimization should indeed take into account particularities of the translational machinery of the tissues in which the target proteins are expressed and that our approach can design genes with tissue-optimized expression profiles. |
HostingRepository | PRIDE |
AnnounceDate | 2023-02-24 |
AnnouncementXML | Submission_2023-02-24_06:47:42.402.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | XavierHernandez Alias |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-10-31 09:27:50 | ID requested | |
⏵ 1 | 2023-02-24 06:47:42 | announced | |
2 | 2023-02-27 06:47:45 | announced | 2023-02-27: Updated project metadata. |
3 | 2023-11-14 07:25:35 | announced | 2023-11-14: Updated project metadata. |
4 | 2023-11-14 08:59:53 | announced | 2023-11-14: Updated project metadata. |
Publication List
Keyword List
submitter keyword: LC-MSMS, PRM, lung, kidney,human |
Contact List
LuisSerrano |
contact affiliation | Systems Biology Unit, Design of Biological Systems, Centre for Genomic Regulation (CRG), Spain |
contact email | luis.serrano@crg.eu |
lab head | |
XavierHernandez Alias |
contact affiliation | Centre de Regulació Genòmica |
contact email | xavier.hernandez@crg.eu |
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/2023/02/PXD037866 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD037866
- Label: PRIDE project
- Name: PRM of eGFP and mCherry in human cells