A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation DOI Creative Commons

Jose Manuel Rodríguez,

Miguel Maquedano, Daniel Cerdán-Vélez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 15, 2024

The human genome has been the subject of intense scrutiny by experimental and manual curation projects for more than two decades. Novel coding genes have proposed from large-scale RNASeq, ribosome profiling proteomics experiments. Here we carry out an in-depth analysis entire database. We analysed proteins, peptides spectra housed in build PeptideAtlas database to identify regions that are not yet annotated GENCODE reference gene set. find support hundreds missing alternative protein isoforms unannotated upstream translations, evidence cross-contamination other species. There was reliable peptide 34 novel open reading frames (ORFs) PeptideAtlas. almost half belong sets. Most remaining ORFs were conserved beyond human, however, their confirmation restricted cancer cell lines. show this is strong aberrant translation, raising important questions about extent translation how these should be genomes.

Language: Английский

CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer DOI Creative Commons

Pengyu Du,

Yingli Chen,

Qian‐Zhong Li

et al.

Database, Journal Year: 2024, Volume and Issue: 2024

Published: Jan. 1, 2024

The discovery of key epigenetic modifications in cancer is great significance for the study disease biomarkers. Through mining modification data relevant to cancer, some researches on are accumulating. In order make it easier integrate effects related cancers, we established CancerMHL (http://www.positionprediction.cn/), which provide DNA methylation, histone and lncRNAs as well effect these gene expression several cancers. To facilitate retrieval, offers flexible query options filters, allowing users access specific according their own needs. addition, based data, three online prediction tools had been offered users. will be a useful resource platform further exploring novel potential biomarkers therapeutic targets cancer. Database URL: http://www.positionprediction.cn/.

Language: Английский

Citations

2
A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation DOI Creative Commons

Jose Manuel Rodríguez,

Miguel Maquedano, Daniel Cerdán-Vélez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 15, 2024

The human genome has been the subject of intense scrutiny by experimental and manual curation projects for more than two decades. Novel coding genes have proposed from large-scale RNASeq, ribosome profiling proteomics experiments. Here we carry out an in-depth analysis entire database. We analysed proteins, peptides spectra housed in build PeptideAtlas database to identify regions that are not yet annotated GENCODE reference gene set. find support hundreds missing alternative protein isoforms unannotated upstream translations, evidence cross-contamination other species. There was reliable peptide 34 novel open reading frames (ORFs) PeptideAtlas. almost half belong sets. Most remaining ORFs were conserved beyond human, however, their confirmation restricted cancer cell lines. show this is strong aberrant translation, raising important questions about extent translation how these should be genomes.

Language: Английский

Citations

2