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Link to original content: http://www.ncbi.nlm.nih.gov/pubmed/34536568
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling - PubMed Skip to main page content
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. 2021 Aug;19(4):602-610.
doi: 10.1016/j.gpb.2021.09.002. Epub 2021 Sep 15.

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling

Yanyan Li  1 , Honghong Zhou  2 , Xiaomin Chen  3 , Yu Zheng  1 , Quan Kang  2 , Di Hao  2 , Lili Zhang  3 , Tingrui Song  2 , Huaxia Luo  2 , Yajing Hao  4 , Runsheng Chen  5 , Peng Zhang  6 , Shunmin He  7
Affiliations

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling

Yanyan Li et al. Genomics Proteomics Bioinformatics. 2021 Aug.

Abstract

Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance of small proteins has been revealed in current years, along with the discovery of their diverse functions. However, systematic annotation of small proteins is still insufficient. SmProt was specially developed to provide valuable information on small proteins for scientific community. Here we present the update of SmProt, which emphasizes reliability of translated sORFs, genetic variants in translated sORFs, disease-specific sORF translation events or sequences, and remarkably increased data volume. More components such as non-ATG translation initiation, function, and new sources are also included. SmProt incorporated 638,958 unique small proteins curated from 3,165,229 primary records, which were computationally predicted from 419 ribosome profiling (Ribo-seq) datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Saccharomyces cerevisiae, Caenorhabditis elegans, and Escherichia coli). In addition, small protein families identified from human microbiomes were also collected. All datasets in SmProt are free to access, and available for browse, search, and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/.

Keywords: Disease; Ribosome profiling; Small open reading frame; Upstream open reading frame; Variants.

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Figures

Figure 1
Figure 1
Construction of SmProt. Items in blue background represent data sources. Items in yellow background represent management processes. Items in red background represent results. WGS, whole genome sequencing; MS, mass spectrometry; TIS, translation initiation site; ORF, open reading frame; sORF, small ORF; uORF, upstream ORF.
Figure 2
Figure 2
Usage of SmProt. SmProt provides multiple ways to search, browse, and visualize small proteins, as well as related diseases and variants.
Figure 3
Figure 3
Contents of SmProt. Detailed information for small proteins are provided, including general annotation, information from ribosome profiling data, literature, other databases, MS, function domain prediction, related diseases, and related variants from WGS projects, as well as corresponding effects.
See this image and copyright information in PMC

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