NDLI: smORFunction: a tool for predicting functions of small open reading frames and microproteins

Content Provider	Springer Nature : BioMed Central
Author	Ji, Xiangwen Cui, Chunmei Cui, Qinghua
Abstract	Background Small open reading frame (smORF) is open reading frame with a length of less than 100 codons. Microproteins, translated from smORFs, have been found to participate in a variety of biological processes such as muscle formation and contraction, cell proliferation, and immune activation. Although previous studies have collected and annotated a large abundance of smORFs, functions of the vast majority of smORFs are still unknown. It is thus increasingly important to develop computational methods to annotate the functions of these smORFs. Results In this study, we collected 617,462 unique smORFs from three studies. The expression of smORF RNAs was estimated by reannotated microarray probes. Using a speed-optimized correlation algorism, the functions of smORFs were predicted by their correlated genes with known functional annotations. After applying our method to 5 known microproteins from literatures, our method successfully predicted their functions. Further validation from the UniProt database showed that at least one function of 202 out of 270 microproteins was predicted. Conclusions We developed a method, smORFunction, to provide function predictions of smORFs/microproteins in at most 265 models generated from 173 datasets, including 48 tissues/cells, 82 diseases (and normal). The tool can be available at https://www.cuilab.cn/smorfunction .
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03805-x.pdf
Ending Page	13
Page Count	13
Starting Page	1
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/s12859-020-03805-x
Journal	BMC Bioinformatics
Issue Number	1
Volume Number	21
Language	English
Publisher	BioMed Central
Publisher Date	2020-10-14
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Small open reading frame Microprotein Function prediction Gene expression Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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