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Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew

View Article: PubMed Central - PubMed

ABSTRACT

The tree shrew (Tupaia belangeri) is a small mammal with a close relationship to primates and it has been proposed as an alternative experimental animal to primates in biomedical research. The recent release of a high-quality Chinese tree shrew genome enables more researchers to use this species as the model animal in their studies. With the aim to making the access to an extensively annotated genome database straightforward and easy, we have created the Tree shrew Database (TreeshrewDB). This is a web-based platform that integrates the currently available data from the tree shrew genome, including an updated gene set, with a systematic functional annotation and a mRNA expression pattern. In addition, to assist with automatic gene sequence analysis, we have integrated the common programs Blast, Muscle, GBrowse, GeneWise and codeml, into TreeshrewDB. We have also developed a pipeline for the analysis of positive selection. The user-friendly interface of TreeshrewDB, which is available at http://www.treeshrewdb.org, will undoubtedly help in many areas of biological research into the tree shrew.

No MeSH data available.


Related in: MedlinePlus

Principal component analysis plot of the global gene expression pattern for tissues from the Chinese tree shrew, including brain, liver, heart, kidney, pancreas, ovary and testis.
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f1: Principal component analysis plot of the global gene expression pattern for tissues from the Chinese tree shrew, including brain, liver, heart, kidney, pancreas, ovary and testis.

Mentions: RPKM (A) refers to mRNA expression of gene A, C is number of reads that uniquely aligned to gene A, N is the total number of reads that were uniquely aligned to all genes, and L is the base number in the CDS of gene A. The RPKM method is able to eliminate the influence of different gene lengths and sequencing discrepancy on the calculation of gene expression. In total, mRNA expression levels of 19,448 genes were detected in at least one of the 7 tissues. We further performed a principal component analysis (PCA) to show the enrichments and relationships among these tissues according to mRNA expression pattern (Figure 1).


Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew
Principal component analysis plot of the global gene expression pattern for tissues from the Chinese tree shrew, including brain, liver, heart, kidney, pancreas, ovary and testis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5382678&req=5

f1: Principal component analysis plot of the global gene expression pattern for tissues from the Chinese tree shrew, including brain, liver, heart, kidney, pancreas, ovary and testis.
Mentions: RPKM (A) refers to mRNA expression of gene A, C is number of reads that uniquely aligned to gene A, N is the total number of reads that were uniquely aligned to all genes, and L is the base number in the CDS of gene A. The RPKM method is able to eliminate the influence of different gene lengths and sequencing discrepancy on the calculation of gene expression. In total, mRNA expression levels of 19,448 genes were detected in at least one of the 7 tissues. We further performed a principal component analysis (PCA) to show the enrichments and relationships among these tissues according to mRNA expression pattern (Figure 1).

View Article: PubMed Central - PubMed

ABSTRACT

The tree shrew (Tupaia belangeri) is a small mammal with a close relationship to primates and it has been proposed as an alternative experimental animal to primates in biomedical research. The recent release of a high-quality Chinese tree shrew genome enables more researchers to use this species as the model animal in their studies. With the aim to making the access to an extensively annotated genome database straightforward and easy, we have created the Tree shrew Database (TreeshrewDB). This is a web-based platform that integrates the currently available data from the tree shrew genome, including an updated gene set, with a systematic functional annotation and a mRNA expression pattern. In addition, to assist with automatic gene sequence analysis, we have integrated the common programs Blast, Muscle, GBrowse, GeneWise and codeml, into TreeshrewDB. We have also developed a pipeline for the analysis of positive selection. The user-friendly interface of TreeshrewDB, which is available at http://www.treeshrewdb.org, will undoubtedly help in many areas of biological research into the tree shrew.

No MeSH data available.


Related in: MedlinePlus