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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

Strategies to identify pathways associated to a miRNA signature. Circles represent protein coding genes and hairpins miRNAs. Gene having the same color of a miRNA are targeted by this miRNA. White genes are not known to be targeted by any miRNA. (a) Strategy 1: targets of the miRNAs of interest are identified using in silico resources and then compared to protein coding genes belonging to each native pathway. (b) Strategy 2: same as strategy 1 but pathways are tailored to only keep genes targeted by at least one miRNA. (c) Strategy 3: pathways of protein coding genes are converted in lists of miRNAs that target at least one of their genes. Then the miRNA signature is directly compared to miRNAs-converted pathways.
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Figure 1: Strategies to identify pathways associated to a miRNA signature. Circles represent protein coding genes and hairpins miRNAs. Gene having the same color of a miRNA are targeted by this miRNA. White genes are not known to be targeted by any miRNA. (a) Strategy 1: targets of the miRNAs of interest are identified using in silico resources and then compared to protein coding genes belonging to each native pathway. (b) Strategy 2: same as strategy 1 but pathways are tailored to only keep genes targeted by at least one miRNA. (c) Strategy 3: pathways of protein coding genes are converted in lists of miRNAs that target at least one of their genes. Then the miRNA signature is directly compared to miRNAs-converted pathways.

Mentions: The most straightforward and widely used strategy to identify pathways associated to a list of miRNAs is to perform an enrichment analysis of the miRNA target genes (Figure 1a) (e.g. (3,4,6–10)). First, genes targeted by any miRNA of interest are identified using a reference database or a prediction algorithm. Then the significance of the overlap between target genes and pathway genes is measured by an enrichment analysis (see ‘Materials and Methods’). This strategy was applied with the AD-up and AD-down lists of miRNAs.


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

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

Strategies to identify pathways associated to a miRNA signature. Circles represent protein coding genes and hairpins miRNAs. Gene having the same color of a miRNA are targeted by this miRNA. White genes are not known to be targeted by any miRNA. (a) Strategy 1: targets of the miRNAs of interest are identified using in silico resources and then compared to protein coding genes belonging to each native pathway. (b) Strategy 2: same as strategy 1 but pathways are tailored to only keep genes targeted by at least one miRNA. (c) Strategy 3: pathways of protein coding genes are converted in lists of miRNAs that target at least one of their genes. Then the miRNA signature is directly compared to miRNAs-converted pathways.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Strategies to identify pathways associated to a miRNA signature. Circles represent protein coding genes and hairpins miRNAs. Gene having the same color of a miRNA are targeted by this miRNA. White genes are not known to be targeted by any miRNA. (a) Strategy 1: targets of the miRNAs of interest are identified using in silico resources and then compared to protein coding genes belonging to each native pathway. (b) Strategy 2: same as strategy 1 but pathways are tailored to only keep genes targeted by at least one miRNA. (c) Strategy 3: pathways of protein coding genes are converted in lists of miRNAs that target at least one of their genes. Then the miRNA signature is directly compared to miRNAs-converted pathways.
Mentions: The most straightforward and widely used strategy to identify pathways associated to a list of miRNAs is to perform an enrichment analysis of the miRNA target genes (Figure 1a) (e.g. (3,4,6–10)). First, genes targeted by any miRNA of interest are identified using a reference database or a prediction algorithm. Then the significance of the overlap between target genes and pathway genes is measured by an enrichment analysis (see ‘Materials and Methods’). This strategy was applied with the AD-up and AD-down lists of miRNAs.

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