PXD053929

PXD053929 is an original dataset announced via ProteomeXchange.

Title	Anti-SMIM45-107aa Pull-down and mass spectrometry study
Description	We acknowledge the commentary by Leushkin et al. on our work, which scrutinizes the status of the de novo genes and the coding potential of a specific case gene (ENSG00000205704) in our proof-of-concept study. While we recognize the evolving nature of defining de novo genes with ribosome profiling data, we respectfully disagree with their assertions for the definition of ages, de novo status, translation and functions of these genes. Notably, the field’s consensus definition of de novo gene is based on the age of the open reading frames (ORFs), rather than that of the locus. Moreover, ribosome profiles alone, although indicative for translation, should not be used as a groundtruth for stable translation and in vivo functions, especially when generated from samples with limited range of temporospatial conditions and analyzed with parameters better suited for highly-expressed, conserved genes, as described in Leushkin et al. Here we present additional data and analyses, especially the verification of the status of these de novo genes and the compelling evidence for in vivo translation of the case gene, to address their concerns. The data presented in our initial report, coupled with this study, robustly support our original conclusions.
HostingRepository	PRIDE
AnnounceDate	2024-08-12
AnnouncementXML	Submission_2024-08-12_03:03:54.879.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chunfu Xiao
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-13 02:09:42	ID requested
⏵ 1	2024-08-12 03:03:55	announced

Dataset with its publication pending

submitter keyword: Human, Pull-down, Fetal brain, SMIM45-107aa

Chuan-Yun Li
contact affiliation	State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China Chinese Institute for Brain Research, Beijing, China Southwest United Graduate School, Kunming 650092, China
contact email	chuanyunli@pku.edu.cn
lab head
Chunfu Xiao
contact affiliation	Peking University
contact email	xiaochunfu@stu.pku.edu.cn
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/2024/08/PXD053929

PRIDE project URI

• PRIDE
  1. PXD053929
     1. Label: PRIDE project
     2. Name: Anti-SMIM45-107aa Pull-down and mass spectrometry study