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rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks
Guo, Liyuan1,2; Wang, Jing1,2
2018-01-04
Source PublicationNUCLEIC ACIDS RESEARCH
Correspondent Emailwangjing@psych.ac.cn ; guoly@psych.ac.cn
ISSN0305-1048
SubtypeArticle
Volume46Issue:D1Pages:D1111-D1116
Contribution Rank1
Abstract

Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks. (ii) Web function was modified according to data content and a new network search module is provided in the rSNPBase 3.0 in addition to the previous regulatory SNP (rSNP) search module. The two search modules support data query for detailed information (related-elements, element-gene pairs, and other extended annotations) on specific SNPs and SNP-related graphic networks constructed by interacting transcription factors (TFs), miRNAs and genes. (3) The type of regulatory elements was modified and enriched. To our best knowledge, the updated rSNPBase 3.0 is the first data tool supports SNP functional analysis from a regulatory network prospective, it will provide both a comprehensive understanding and concrete guidance for SNP-related regulatory studies.

DOI10.1093/nar/gkx1101
Indexed BySCI
Language英语
Funding OrganizationCAS 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) ; National Natural Science Foundation of China(81201046)
WOS Research AreaBiochemistry & Molecular Biology
WOS SubjectBiochemistry & Molecular Biology
WOS IDWOS:000419550700159
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
WOS KeywordTRANSCRIPTION FACTOR ; SIGNAL-TRANSDUCTION ; MICRORNA ; EXPRESSION ; GENOME ; VARIANTS ; SEQUENCE ; DISEASE ; TARGETS ; CANCER
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Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.psych.ac.cn/handle/311026/22302
Collection中国科学院心理健康重点实验室
Affiliation1.Chinese Acad Sci, Inst Psychol, CAS Key Lab Mental Hlth, Beijing 100101, Peoples R China
2.Univ Chinese Acad Sci, Dept Psychol, Beijing 100049, Peoples R China
Recommended Citation
GB/T 7714
Guo, Liyuan,Wang, Jing. rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks[J]. NUCLEIC ACIDS RESEARCH,2018,46(D1):D1111-D1116.
APA Guo, Liyuan,&Wang, Jing.(2018).rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks.NUCLEIC ACIDS RESEARCH,46(D1),D1111-D1116.
MLA Guo, Liyuan,et al."rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks".NUCLEIC ACIDS RESEARCH 46.D1(2018):D1111-D1116.
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