PXD023558

PXD023558 is an original dataset announced via ProteomeXchange.

Title	A genome-wide atlas of co-essential modules assigns function to uncharacterized genes
Description	A 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.
HostingRepository	PRIDE
AnnounceDate	2022-02-16
AnnouncementXML	Submission_2022-02-16_12:55:41.847.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Roarke Kamber
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-12 23:57:32	ID requested
⏵ 1	2022-02-16 12:55:42	announced

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]

submitter keyword: IP-MS, TMEM189, C15orf57

Michael Bassik
contact affiliation	Department of Genetics, Stanford University
contact email	bassik@stanford.edu
lab head
Roarke Kamber
contact affiliation	Stanford University
contact email	rakamber@stanford.edu
dataset submitter

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/2022/02/PXD023558

PRIDE project URI

• PRIDE
  1. PXD023558
     1. Label: PRIDE project
     2. Name: A genome-wide atlas of co-essential modules assigns function to uncharacterized genes