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COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.

Okamura Y, Aoki Y, Obayashi T, Tadaka S, Ito S, Narise T, Kinoshita K - Nucleic Acids Res. (2014)

Bottom Line: For the second point, we refined the data assessment procedures, for each coexpressed gene list and for the total performance of a platform.The assessment of coexpressed gene list now uses more reasonable P-values derived from platform-specific distribution.These developments greatly reduced pseudo-predictions for directly associated genes, thus expanding the reliability of coexpression data to design new experiments and to discuss experimental results.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.

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Related in: MedlinePlus

Number of guide genes for each supportability level. Supportability levels are represented as stars, where no star is the lowest and a triple star is the highest. Numbers in the bars indicate the percentage of each supportability level in each platform. Genes without any reference genes in the other platforms are shown as a blank box.
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Figure 1: Number of guide genes for each supportability level. Supportability levels are represented as stars, where no star is the lowest and a triple star is the highest. Numbers in the bars indicate the percentage of each supportability level in each platform. Genes without any reference genes in the other platforms are shown as a blank box.

Mentions: The numbers of genes at each significance level are summarized in Figure 1. Human, mouse and fly show higher populations of high supportability level genes than the other species, reflecting the fact that these species have multiple platforms that are most suitable to prove the reliability of the coexpressed gene lists. Note that ‘No star’ does not always mean unreliable. ‘No star’ is also available for coexpression specifically observed in the species, or it may just result from the lack of an appropriate reference platform. Even so, for general purposes, a high supportability level of coexpression is recommended to prioritize genes. As the human platforms have strong coexpression support (Figure 1), the human coexpression data in COXPRESdb are one of the most important resources for human research.


COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.

Okamura Y, Aoki Y, Obayashi T, Tadaka S, Ito S, Narise T, Kinoshita K - Nucleic Acids Res. (2014)

Number of guide genes for each supportability level. Supportability levels are represented as stars, where no star is the lowest and a triple star is the highest. Numbers in the bars indicate the percentage of each supportability level in each platform. Genes without any reference genes in the other platforms are shown as a blank box.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383961&req=5

Figure 1: Number of guide genes for each supportability level. Supportability levels are represented as stars, where no star is the lowest and a triple star is the highest. Numbers in the bars indicate the percentage of each supportability level in each platform. Genes without any reference genes in the other platforms are shown as a blank box.
Mentions: The numbers of genes at each significance level are summarized in Figure 1. Human, mouse and fly show higher populations of high supportability level genes than the other species, reflecting the fact that these species have multiple platforms that are most suitable to prove the reliability of the coexpressed gene lists. Note that ‘No star’ does not always mean unreliable. ‘No star’ is also available for coexpression specifically observed in the species, or it may just result from the lack of an appropriate reference platform. Even so, for general purposes, a high supportability level of coexpression is recommended to prioritize genes. As the human platforms have strong coexpression support (Figure 1), the human coexpression data in COXPRESdb are one of the most important resources for human research.

Bottom Line: For the second point, we refined the data assessment procedures, for each coexpressed gene list and for the total performance of a platform.The assessment of coexpressed gene list now uses more reasonable P-values derived from platform-specific distribution.These developments greatly reduced pseudo-predictions for directly associated genes, thus expanding the reliability of coexpression data to design new experiments and to discuss experimental results.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.

Show MeSH
Related in: MedlinePlus