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PXD023558 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleA genome-wide atlas of co-essential modules assigns function to uncharacterized genes
DescriptionA central remaining question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into ‘co-essential’ pathways, but this approach has been limited by ubiquitous false positives. Here, we develop a statistical method that enables robust identification of gene co-essentiality and yields a genome-wide set of functional modules. This atlas recapitulates diverse pathways and protein complexes and predicts the functions of 155 uncharacterized genes. Validating top predictions, we show that TMEM189 encodes plasmanylethanolamine desaturase, the long-sought key enzyme for plasmalogen synthesis. We also show that C15orf57 binds the AP2 complex, localizes to clathrin-coated pits, and enables efficient transferrin uptake. Finally, we provide an interactive web tool for the community to explore our results. Our results establish co-essentiality profiling as a powerful resource for biological pathway identification and discovery of novel gene functions.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterRoarke Kamber
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentLTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-01-12 23:57:32ID requested
12022-02-16 12:55:42announced
Publication List
Wainberg M, Kamber RA, Balsubramani A, Meyers RM, Sinnott-Armstrong N, Hornburg D, Jiang L, Chan J, Jian R, Gu M, Shcherbina A, Dubreuil MM, Spees K, Meuleman W, Snyder MP, Bassik MC, Kundaje A, A genome-wide atlas of co-essential modules assigns function to uncharacterized genes. Nat Genet, 53(5):638-649(2021) [pubmed]
Keyword List
submitter keyword: IP-MS, TMEM189, C15orf57
Contact List
Michael Bassik
contact affiliationDepartment of Genetics, Stanford University
contact emailbassik@stanford.edu
lab head
Roarke Kamber
contact affiliationStanford University
contact emailrakamber@stanford.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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