PXD030066

PXD030066 is an original dataset announced via ProteomeXchange.

Title	LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism
Description	The dual functional lncRNAs have been intensively studied and identified to be involved in various fundamental cellular processes recently. It is essential to understand in which context when a dual functional lncRNA serves as a non-coding RNA or a template for coding peptide, particularly in some pathological conditions. However, apart from time consuming and cell type specific experiments, there is virtually no in-silico method for predicting the identity of dual functional lncRNAs. Here, we developed a deep-learning model with multi-head self-attention mechanism, LncReader, to identify dual functional lncRNAs based on their sequence, physicochemical and secondary structural features. Our data demonstrated that LncReader showed multiple advantage compared to various classical machine learning methods. Moreover, to obtain independent in-house datasets for robust testing, mass spectrometry proteomics combined with RNA-seq were applied in four leukemia cell lines. Remarkably, LncReader achieved the best performance among all these datasets. Therefore, LncReader provides a sophisticated and practical tool that enables fast dual functional lncRNAs identification.
HostingRepository	PRIDE
AnnounceDate	2024-02-12
AnnouncementXML	Submission_2024-02-12_09:03:47.075.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tianyuan Liu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Thermo Fisher Scientific instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-30 08:39:08	ID requested
⏵ 1	2024-02-12 09:03:49	announced

10.1093/bib/bbac579;

Liu T, Zou B, He M, Hu Y, Dou Y, Cui T, Tan P, Li S, Rao S, Huang Y, Liu S, Cai K, Wang D, LncReader: identification of dual functional long noncoding RNAs using a multi-head self-attention mechanism. Brief Bioinform, 24(1):(2023) [pubmed]

submitter keyword: THP_1,leukemia cell lines, K562, HL60, MOLM13

Dong Wang
contact affiliation	Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
contact email	wangdong79@smu.edu.cn
lab head
Tianyuan Liu
contact affiliation	Southern Medical University
contact email	biocoder1024@hotmail.com
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/2023/04/PXD030066

PRIDE project URI

• PRIDE
  1. PXD030066
     1. Label: PRIDE project
     2. Name: LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism