sTAM: An Online Tool for the Discovery of miRNA-Set Level Disease Biomarkers
MicroRNAs (miRNAs) are an important class of small noncoding RNA molecules that serve as excellent biomarkers of various diseases. However, current miRNA biomarkers, including those comprised of multiple miRNAs, work at a single-miRNA level but not at a miRNA-set level, which is defined as a group o...
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doaj-613abe62eb834f0483f2a78064b74bcb2020-11-25T03:18:58ZengElsevierMolecular Therapy: Nucleic Acids2162-25312020-09-0121670675sTAM: An Online Tool for the Discovery of miRNA-Set Level Disease BiomarkersJiangcheng Shi0Qinghua Cui1Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd., Beijing 100191, ChinaDepartment of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd., Beijing 100191, China; Corresponding author: Qinghua Cui, Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd., Beijing 100191, China.MicroRNAs (miRNAs) are an important class of small noncoding RNA molecules that serve as excellent biomarkers of various diseases. However, current miRNA biomarkers, including those comprised of multiple miRNAs, work at a single-miRNA level but not at a miRNA-set level, which is defined as a group of miRNAs sharing common biological characteristics. Given the rapidly accumulating miRNA omics data, we believe that the miRNA-set level analysis could be an important supplement to the single-miRNA level analysis. Therefore, we present sTAM (http://mir.rnanut.net/stam), a computational tool for single-sample miRNA-set enrichment analysis. Moreover, we demonstrate the utility of sTAM scores in discovering miRNA-set level biomarkers through two case studies. We conduct a pan-cancer analysis of the sTAM scores of the “tumor suppressor miRNA set” on 15 types of cancers from The Cancer Genome Atlas (TCGA) and 14 from Gene Expression Omnibus (GEO), results of which indicated a good performance in distinguishing cancers from controls. Moreover, we reveal that the sTAM scores of the “brain development miRNA set” can effectively predict cerebrovascular disorder (CVD). Finally, we believe that sTAM can be used to discover disease-related biomarkers at a miRNA-set level.http://www.sciencedirect.com/science/article/pii/S2162253120301931miRNA setbiomarkersingle-sample enrichment analysisgene expression |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jiangcheng Shi Qinghua Cui |
spellingShingle |
Jiangcheng Shi Qinghua Cui sTAM: An Online Tool for the Discovery of miRNA-Set Level Disease Biomarkers Molecular Therapy: Nucleic Acids miRNA set biomarker single-sample enrichment analysis gene expression |
author_facet |
Jiangcheng Shi Qinghua Cui |
author_sort |
Jiangcheng Shi |
title |
sTAM: An Online Tool for the Discovery of miRNA-Set Level Disease Biomarkers |
title_short |
sTAM: An Online Tool for the Discovery of miRNA-Set Level Disease Biomarkers |
title_full |
sTAM: An Online Tool for the Discovery of miRNA-Set Level Disease Biomarkers |
title_fullStr |
sTAM: An Online Tool for the Discovery of miRNA-Set Level Disease Biomarkers |
title_full_unstemmed |
sTAM: An Online Tool for the Discovery of miRNA-Set Level Disease Biomarkers |
title_sort |
stam: an online tool for the discovery of mirna-set level disease biomarkers |
publisher |
Elsevier |
series |
Molecular Therapy: Nucleic Acids |
issn |
2162-2531 |
publishDate |
2020-09-01 |
description |
MicroRNAs (miRNAs) are an important class of small noncoding RNA molecules that serve as excellent biomarkers of various diseases. However, current miRNA biomarkers, including those comprised of multiple miRNAs, work at a single-miRNA level but not at a miRNA-set level, which is defined as a group of miRNAs sharing common biological characteristics. Given the rapidly accumulating miRNA omics data, we believe that the miRNA-set level analysis could be an important supplement to the single-miRNA level analysis. Therefore, we present sTAM (http://mir.rnanut.net/stam), a computational tool for single-sample miRNA-set enrichment analysis. Moreover, we demonstrate the utility of sTAM scores in discovering miRNA-set level biomarkers through two case studies. We conduct a pan-cancer analysis of the sTAM scores of the “tumor suppressor miRNA set” on 15 types of cancers from The Cancer Genome Atlas (TCGA) and 14 from Gene Expression Omnibus (GEO), results of which indicated a good performance in distinguishing cancers from controls. Moreover, we reveal that the sTAM scores of the “brain development miRNA set” can effectively predict cerebrovascular disorder (CVD). Finally, we believe that sTAM can be used to discover disease-related biomarkers at a miRNA-set level. |
topic |
miRNA set biomarker single-sample enrichment analysis gene expression |
url |
http://www.sciencedirect.com/science/article/pii/S2162253120301931 |
work_keys_str_mv |
AT jiangchengshi stamanonlinetoolforthediscoveryofmirnasetleveldiseasebiomarkers AT qinghuacui stamanonlinetoolforthediscoveryofmirnasetleveldiseasebiomarkers |
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