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Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy.

Godard P, van Eyll J - Nucleic Acids Res. (2015)

Bottom Line: MicroRNAs (miRNAs) are involved in the regulation of gene expression at a post-transcriptional level.In large scale studies, once miRNAs of interest have been identified, the target genes they regulate are often inferred using algorithms or databases.A pathway analysis is then often performed in order to generate hypotheses about the relevant biological functions controlled by the miRNA signature.

View Article: PubMed Central - PubMed

Affiliation: IP & Science, Thomson Reuters, 5901 Priestly Drive, #200, Carlsbad, CA 92008, USA.

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Related in: MedlinePlus

Pathways enriched in the top 500 genes targeted by miRNAs according to MetaBase, TargetScan or mirTarBase when applying strategy 2. Numbers in red correspond to KEGG pathways and those in blue to MetaBase pathways.
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Figure 3: Pathways enriched in the top 500 genes targeted by miRNAs according to MetaBase, TargetScan or mirTarBase when applying strategy 2. Numbers in red correspond to KEGG pathways and those in blue to MetaBase pathways.

Mentions: Again, to check the dependence of this result toward the tools and databases, the same workflow was applied using alternative resources. The same kind of bias is observed when using other sources for miRNA target identification and when performing the enrichment analysis on the MetaBase pathways (Figure 3). This result indicates that this bias is related to the method as such and not to the knowledge resources it uses.


Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy.

Godard P, van Eyll J - Nucleic Acids Res. (2015)

Pathways enriched in the top 500 genes targeted by miRNAs according to MetaBase, TargetScan or mirTarBase when applying strategy 2. Numbers in red correspond to KEGG pathways and those in blue to MetaBase pathways.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402548&req=5

Figure 3: Pathways enriched in the top 500 genes targeted by miRNAs according to MetaBase, TargetScan or mirTarBase when applying strategy 2. Numbers in red correspond to KEGG pathways and those in blue to MetaBase pathways.
Mentions: Again, to check the dependence of this result toward the tools and databases, the same workflow was applied using alternative resources. The same kind of bias is observed when using other sources for miRNA target identification and when performing the enrichment analysis on the MetaBase pathways (Figure 3). This result indicates that this bias is related to the method as such and not to the knowledge resources it uses.

Bottom Line: MicroRNAs (miRNAs) are involved in the regulation of gene expression at a post-transcriptional level.In large scale studies, once miRNAs of interest have been identified, the target genes they regulate are often inferred using algorithms or databases.A pathway analysis is then often performed in order to generate hypotheses about the relevant biological functions controlled by the miRNA signature.

View Article: PubMed Central - PubMed

Affiliation: IP & Science, Thomson Reuters, 5901 Priestly Drive, #200, Carlsbad, CA 92008, USA.

Show MeSH
Related in: MedlinePlus