ArticleFrontiers in genetics2018
FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions.
Article in Frontiers in genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 29 citations in OpenAlex.
- High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.Nature communications · 2026Article
- Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery.Nature protocols · 2025Review
- SProtFP: a machine learning-based method for functional classification of small ORFs in prokaryotes.NAR genomics and bioinformatics · 2025Article
- Noncanonical microprotein regulation of immunity.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Review
- Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome.Genome biology · 2024Article
- Integrated sequence and -omic features reveal novel small proteome ofFrontiers in microbiology · 2024Article
- IRSOM2: a web server for predicting bifunctional RNAs.Nucleic acids research · 2023Article
- Understanding small ORF diversity through a comprehensive transcription feature classification.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Review
- smORFunction: a tool for predicting functions of small open reading frames and microproteins.BMC bioinformatics · 2020Article
- LncRNA-Encoded Peptide: Functions and Predicting Methods.Frontiers in oncology · 2020Review
- Small Open Reading Frames: How Important Are They for Molecular Evolution?Frontiers in genetics · 2020Article
- SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- CPPred: coding potential prediction based on the global description of RNA sequence.Nucleic acids research · 2019Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
smORFs are small open reading frames of less than 100 codons. Recent low throughput experiments showed a lot of smORF-encoded peptides (SEPs) played crucial rule in processes such as regulation of transcription or translation, transportation through membranes and the antimicrobial activity. In order to gather more functional SEPs, it is necessary to have access to genome-wide prediction tools to give profound directions for low throughput experiments. In this study, we put forward a functional smORF-encoded peptides predictor (FSPP) which tended to predict authentic SEPs and their functions in a high throughput method. FSPP used the overlap of detected SEPs from Ribo-seq and mass spectrometry as target objects. With the expression data on transcription and translation levels, FSPP built two co-expression networks. Combing co-location relations, FSPP constructed a compound network and then annotated SEPs with functions of adjacent nodes. Tested on 38 sequenced samples of 5 human cell lines, FSPP successfully predicted 856 out of 960 annotated proteins. Interestingly, FSPP also highlighted 568 functional SEPs from these samples. After comparison, the roles predicted by FSPP were consistent with known functions. These results suggest that FSPP is a reliable tool for the identification of functional small peptides. FSPP source code can be acquired at https://www.bioinfo.org/FSPP.
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