Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology
Institute of Biophysics
Chinese Academy of Sciences
15 Datun Road, Chaoyang District
Beijing 100101, China
SpatialDB is supported by CAS Key Technology Talent Program, National Natural Science Foundation of China [31871307, 31801072, 31701122 and 31520103905], National Key Research and Development Project [2018YFA0106901].
Our previous work
1. LncVar: a database of genetic variation associated with long non-coding genes. (http://188.8.131.52/LncVar/)
Long noncoding RNAs (lncRNAs) have been identified in various species, and play essential roles in many molecular processes. Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome. Variations in the long noncoding gene loci may affect lncRNA transcripts from sequences, structures, expression levels to biological functions.Therefore we constructed
LncVar, a database of long noncoding genes associated genetic variations in 6 species (human, mouse, zebrafish, worm, fruitfly, Arabidopsis).
1. Chen X., et al. LncVar: a database of genetic variation associated with long non-coding genes. Bioinformatics. 2017 Jan 1;33(1):112-118. doi: 10.1093/bioinformatics/btw581. Epub 2016 Sep 6. PubMed PMID: 27605101.
2. Chen X., et al. LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes. Methods Mol Biol. 2019;1870:189-198. doi:10.1007/978-1-4939-8808-2_14. PubMed PMID: 30539556.
2. RefCirc: a reference database for circRNAs validated by experiments. (http://www.ncvar.org/RefCirc/)
RefCirc database is a manually curated database for circRNAs validated by experiments. RefCirc provides basic information, expression, function, interaction and reference for circRNAs. The basic information includes circRNA name, alias, circBase ID, host gene, species, ORF and sequence. The expression section contains the description of circRNA expression, experimental methods and samples. The function section includes the description of circRNA function, experimental methods and samples. The interaction section includes circRNA interaction targets, description of interaction, experimental methods and samples. The reference section contains the PMID, related traits/diseases, paper title, authors and journal. The current version of RefCirc contains 1,583 circRNAs in 20 species.
1. Fan Z. and Chen X. (2018, July 1). RefCirc: a reference database for circRNAs validated by experiments. Retrieved from http://www.ncvar.org/RefCirc/