MTD: A mammalian transcriptomic database to explore gene expression and regulation

Briefings in Bioinformatics

Volumn 18, Issue 1, 2017, Pages 28-36

  Sheng, Xin ^a   Wu, Jiayan ^b   Sun, Qianqian ^a   Li, Xue ^a   Xian, Feng ^a   Sun, Manman ^c   Fang, Wan ^a   Chen, Meili ^b   Yu, Jun ^b   Xiao, Jingfa ^b  

^a UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^b Chinese Academy of Sciences   (China)

^c HUNAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

Gene expression and regulation; Mammalian transcriptomic database; RNA seq

Indexed keywords

TRANSCRIPTOME;

ANIMAL; EXON; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENOME; GENOMICS; HUMAN; MOUSE; PIG; RAT;

ANIMALS; DATABASES, GENETIC; EXONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME; GENOMICS; HUMANS; MICE; RATS; SWINE; TRANSCRIPTOME;

EID: 85015966988     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbv117     Document Type: Article

References (25)

1. Adams J. Transcriptome: connecting the genome to gene function. Nat Educ 2008;1:195.
2. Chen M, Xiao J, Zhang Z, et al. Identification of human HK genes and gene expression regulation study in cancer from transcriptomics data analysis. PloS One 2013;8:e54082.
3. Zhu J, He F, Wang D, et al. A novel role for minimal introns: routing mrnas to the cytosol. PloS One 2010;5:e10144.
4. Cui P, Lin Q, Ding F, et al. The transcript-centric mutations in human genomes. Genomics Proteomics Bioinformatics 2012;10:11-22.
5. Cui P, Liu W, Zhao Y, et al. The association between H3K4me3 and antisense transcription. Genomics Proteomics Bioinformatics 2012;10:74-81.
6. Cui P, Ding F, Lin Q, et al. Distinct contributions of replication and transcription to mutation rate variation of human genomes. Genomics Proteomics Bioinformatics 2012;10:4-10.
7. Eisenberg E, Levanon EY. Human housekeeping genes, revisited. Trends Genet 2013;29:569-74.
8. Barbosa-Morais NL, Irimia M, Pan Q, et al. The evolutionary landscape of alternative splicing in vertebrate species. Science 2012;338:1587-93.
9. Merkin J, Russell C, Chen P, et al. Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 2012;338:1593-9.
10. Reyes A, Anders S, Weatheritt RJ, et al. Drift and conservation of differential exon usage across tissues in primate species. Proc Natl Acad Sci USA 2013;110:15377-82.
11. Lin S, Lin Y, Nery JR, et al. Comparison of the transcriptional landscapes between human and mouse tissues. Proc Natl Acad Sci USA 2014;111:17224-9.
12. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10:57-63.
13. Miranda-Saavedra D, De S, Trotter MW, et al. BloodExpress: a database of gene expression in mouse haematopoiesis. Nucleic Acids Res 2009;37:D873-9.
14. Sunkin SM, Ng L, Lau C, et al. Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system. Nucleic Acids Res 2013;41:D996-1008.
15. Zhao D, Wu J, Zhou Y, et al. WikiCell: a unified resource platform for human transcriptomics research. OMICS 2012;16:357-62.
16. Richardson L, Venkataraman S, Stevenson P, et al. EMAGE mouse embryo spatial gene expression database: 2014 update. Nucleic Acids Res 2014;42:D835-44.
17. Peng XX, Thierry-Mieg J, Thierry-Mieg D, et al. Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). Nucleic Acids Res 2015;43:D737-42.
18. Petryszak R, Burdett T, Fiorelli B, et al. Expression Atlas update-a database of gene and transcript expression from microarray-and sequencing-based functional genomics experiments. Nucleic Acids Res 2014;42:D926-32.
19. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctionswith RNA-Seq. Bioinformatics 2009;25:1105-11.
20. Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012;7:562-78.
21. Mortazavi A, Williams BA, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008;5:621-8.
22. Stein LD, Mungall C, Shu SQ, et al. The generic genome browser: a building block for a model organism system database. Genome Res 2002;12:1599-610.
23. Kanehisa M, Goto S, Sato Y, et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 2014;42:D199-205.
24. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178-89.
25. Zhu J, He FH, Song SH, et al. How many human genes can be defined as housekeeping with current expression data? BMC Genomics 2008;9:11.