PepPSy: a web server to prioritize gene products in experimental and biocuration workflows

Sallou, Olivier; Duek, Paula D.; Darde, Thomas Alain; Collin, Olivier; Lane, Lydie; Chalmel, Frédéric

doi:10.1093/database/baw070

Cited by 2 publications

(2 citation statements)

References 33 publications

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“…Four linc-genes ( LINC00305 , LINC00470 , LINC00526 , and LINC01387 ) encode open-reading frames of uncharacterized chromosome-specific proteins C18orf20, C18orf2, C18orf18, and C18orf64, respectively. However, their protein existence status remains ‘uncertain’ according to the PepPsy portal [ 22 ]. LincRNAs-of-interest in the form of circRNAs, a type of single-stranded RNA forming a covalently closed continuous loop, were not found in the ‘Circular RNA Interactome’ [ 23 ] and ‘CircBank’ [ 24 ] databases.…”

Section: A Spectrum Of Genes Encoding Lincrnas Of Human Chromosome 18mentioning

confidence: 99%

Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers

Ershov,

Yablokov,

Mezentsev

et al. 2024

Biomedicines

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Malignant neoplasms are characterized by high molecular heterogeneity due to multilevel deregulation of gene expression and cellular functions. It is known that non-coding RNAs, including long intergenic non-coding RNAs (lincRNAs), can play significant roles in cancer biology. The current review focuses on a systematical analysis of genomic, transcriptomic, epigenomic, interactomic, and literature data on 65 lincRNAs of human chromosome 18 in the context of pan-cancer studies. The entire group of lincRNAs can be conditionally divided into 4 subgroups depending on experimental evidence on direct or indirect involvement in cancers and the biological associations with cancers, which we found during the data-mining process: the most studied (5 lincRNAs), moderately or poorly studied (11 lincRNAs), and understudied (31 lincRNAs). For the remaining 18 lincRNAs, data for analysis were fragmentary or missing. Among the key findings were the following: Of the lincRNAs of human chromosome 18, 40% have tissue-specific expression patterns, 22% of lincRNAs are known to have gene fusions, 40% of lincRNAs are prone to gene amplifications and/or deletions in cancers at a frequency greater than 3%, and 23% of lincRNAs are differentially expressed across cancer types, whereas 7% have subtype-specific expression patterns. LincRNAs’ interactomes consist of ‘master’ microRNAs and 47 proteins (including cancer-associated proteins and microRNAs) that can interact with 3 or more lincRNAs. Functional enrichment analysis of a set of highly co-expressed genes retrieved for 17 lincRNAs in different cancer types indicated the potential associations of these lincRNAs with cellular signaling pathways. Six lincRNAs encoded small open-reading frame (smORF) proteins with emerging roles in cancers, and microRNAs as well as proteins with known functions in molecular carcinogenesis can bind to coding regions of smORFs. We identified seven transcriptomic signatures with potential prognostic value, consisting of two to seven different lincRNAs only. Taken together, the literature, biomedical, and molecular biology data analyzed indicated that only five of all lincRNAs of human chromosome 18 are cancer-associated, while eleven other lincRNAs have the tendency to be associated with cancers.

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Section: A Spectrum Of Genes Encoding Lincrnas Of Human Chromosome 18mentioning

confidence: 99%

Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers

Ershov,

Yablokov,

Mezentsev

et al. 2024

Biomedicines

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“…Data on protein expression in normal tissues were obtained from the PepPSy server [87], URL: http://peppsy.genouest.org/query (accessed on 6 February 2023). This server enables the determining in which human tissues investigators should look for unseen ('missing') proteins.…”

Section: Protein Expression Data Analysismentioning

confidence: 99%

Uncharacterized Proteins CxORFx: Subinteractome Analysis and Prognostic Significance in Cancers

Ершов

Yablokov

Mezentsev

et al. 2023

IJMS

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Functions of about 10% of all the proteins and their associations with diseases are poorly annotated or not annotated at all. Among these proteins, there is a group of uncharacterized chromosome-specific open-reading frame genes (CxORFx) from the ‘Tdark’ category. The aim of the work was to reveal associations of CxORFx gene expression and ORF proteins’ subinteractomes with cancer-driven cellular processes and molecular pathways. We performed systems biology and bioinformatic analysis of 219 differentially expressed CxORFx genes in cancers, an estimation of prognostic significance of novel transcriptomic signatures and analysis of subinteractome composition using several web servers (GEPIA2, KMplotter, ROC-plotter, TIMER, cBioPortal, DepMap, EnrichR, PepPSy, cProSite, WebGestalt, CancerGeneNet, PathwAX II and FunCoup). The subinteractome of each ORF protein was revealed using ten different data sources on physical protein–protein interactions (PPIs) to obtain representative datasets for the exploration of possible cellular functions of ORF proteins through a spectrum of neighboring annotated protein partners. A total of 42 out of 219 presumably cancer-associated ORF proteins and 30 cancer-dependent binary PPIs were found. Additionally, a bibliometric analysis of 204 publications allowed us to retrieve biomedical terms related to ORF genes. In spite of recent progress in functional studies of ORF genes, the current investigations aim at finding out the prognostic value of CxORFx expression patterns in cancers. The results obtained expand the understanding of the possible functions of the poorly annotated CxORFx in the cancer context.

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PepPSy: a web server to prioritize gene products in experimental and biocuration workflows

Cited by 2 publications

References 33 publications

Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers

Long Intergenic Non-Coding RNAs of Human Chromosome 18: Focus on Cancers

Uncharacterized Proteins CxORFx: Subinteractome Analysis and Prognostic Significance in Cancers

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