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BEST: a web server for brain expression Spatio-temporal pattern analysis
Guo, Liyuan1,2; Lin, Wei1,2; Zhang, Yidan1,2; Li, Wenhan3; Wang, Jing1,2
First AuthorGuo, Liyuan
Correspondent Emailwangjing@psych.ac.cn
Contribution Rank1
Abstract

Background: Dysregulated gene expression patterns have been reported in several mental disorders. Limited by the difficulty of obtaining samples, psychiatric molecular mechanism research still relies heavily on clues from genetics studies. By using reference data from brain expression studies, multiple types of comprehensive gene expression pattern analysis have been performed on psychiatric genetic results. These systems-level spatial-temporal expression pattern analyses provided evidence on specific brain regions, developmental stages and molecular pathways that are possibly involved in psychiatric pathophysiology. At present, there is no online tool for such systematic analysis, which hinders the applications of analysis by non-informatics researchers such as experimental biologists and clinical molecular biologists. Results: We developed the BEST web server to support Brain Expression Spatio-Temporal pattern analysis. There are three highlighted features of BEST: 1) visualization: it generates user-friendly visual results that are easy to interpret, including heatmaps, Venn diagrams, gene co-expression networks and cluster-based Manhattan gene plots; these results illustrate the complex spatio-temporal expression patterns, including expression quantification and correlation between genes; 2) integration: it provides comprehensive human brain spatio-temporal expression patterns by integrating data from currently available databases; 3) multi-dimensionality: it analyses input genes as both a whole set and several subsets (clusters) which are enriched according to co-expression patterns, and it also presents the correlation between genetic and expression data. Conclusions: To the best of our knowledge, BEST is the first data tool to support comprehensive human brain spatial-temporal expression pattern analysis. It helps to bridge disease-related genetic studies and mechanism studies, provides clues for key gene and molecular system identification, and supports the analysis of disease sensitive brain region and age stages.

KeywordWeb server Brain expression pattern analysis Spatio-temporal Co-expression cluster Visualization
2019-12-05
Language英语
DOI10.1186/s12859-019-3222-6
Source PublicationBMC BIOINFORMATICS
ISSN1471-2105
Volume20Issue:1Pages:8
SubtypeArticle
Indexed BySCI
Funding ProjectNational Basic Research (973) Program[2015CB351702] ; CAS Key Laboratory of Mental Health, Institute of Psychology ; CAS/SAFEA International Partnership Program for Creative Research Teams[Y2CX131003] ; Knowledge Innovation Program of the Chinese Academy of Sciences[KSCX2-EW-J-8]
PublisherBMC
WOS KeywordGENE ; TRANSCRIPTOME ; ATLAS ; LAYERS
WOS Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS SubjectBiochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS IDWOS:000511608300001
QuartileQ1
Citation statistics
Document Type期刊论文
Identifierhttp://ir.psych.ac.cn/handle/311026/30403
Collection中国科学院心理健康重点实验室
Corresponding AuthorWang, Jing
Affiliation1.Chinese Acad Sci, Inst Psychol, CAS Key Lab Mental Hlth, 16 Lincui Rd, Beijing 100101, Peoples R China
2.Univ Chinese Acad Sci, Dept Psychol, Beijing 100049, Peoples R China
3.Oumeng V Med Lab, Hangzhou 310013, Zhejiang, Peoples R China
First Author AffilicationKey Laboratory of Mental Health, CAS
Corresponding Author AffilicationKey Laboratory of Mental Health, CAS
Recommended Citation
GB/T 7714
Guo, Liyuan,Lin, Wei,Zhang, Yidan,et al. BEST: a web server for brain expression Spatio-temporal pattern analysis[J]. BMC BIOINFORMATICS,2019,20(1):8.
APA Guo, Liyuan,Lin, Wei,Zhang, Yidan,Li, Wenhan,&Wang, Jing.(2019).BEST: a web server for brain expression Spatio-temporal pattern analysis.BMC BIOINFORMATICS,20(1),8.
MLA Guo, Liyuan,et al."BEST: a web server for brain expression Spatio-temporal pattern analysis".BMC BIOINFORMATICS 20.1(2019):8.
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