MiRNA feed forward loops (analysis)

Analysis title

miRNA feed forward loops

Provider

geneXplain GmbH

Class

MiRNAFeedForwardLoops

Plugin

com.genexplain.analyses (geneXplain analyses)

Finds miRNA feed forward loops.

The miRNA feed forward loop is a combination of miRNA, a transcription factor and a target gene. The miRNA regulates target gene. The transcription factor regulates transcription of both target gene and gene encoding miRNA. This analysis accepts the list of miRNA or the list of target genes or both and finds corresponding miRNA feed forward loops.

Regulation by the given transcription factor of corresponding gene is estimated by computing the regulation score for the promoter of gene and comparing this score to the distribution of the regulation scores in the background gene set. The regulation score can be computed in two different ways:

• Site count - the score is the number of binding sites found in promoter region using supplied siteModelCollection(profile)
• MEALR - the score is the sum of PWM scores for each position in promoter normalized by the length of promoter.

To compare obtained regulation score with distribution of scores in the background gene set, the fraction of bacground genes having greater scores is computed. And promoter score = -log₁₀(fraction). miRNAPromoterScore and targetGenePromoterScore is computed in this way (greater is better).

The data about regulation of target gene by miRNA is taken from TargetScan(GeneXplain) database. The database provides numerical scores for each regulation event. This analysis computes the fraction of TargetScan regulation events with the score greater then score of current event. And miRNATargetScore = -log₁₀(fraction). Greater miRNATargetScore is better.

The finalScore of miRNA feed forward loop is a sum of miRNAPromoterScore + targetGenePromoterScore + miRNATargetScore. Potential miRNA feed forward loops are reported only if they pass four conditions:

• miRNAPromoterScore >= RNAPromoterScoreThreshold
• targetGenePromoterScore >= targetGenePromoterScoreThreshold
• miRNATargetScore >= miRNATargetScoreThreshold
• finalScore >= scoreThreshold

Parameters:

• miRNAs – miRNAs
• targetGenes – targetGenes
• siteModelCollection – siteModelCollection
• ensembl – ensembl
• scoreType – scoreType
• backgroundGenes – backgroundGenes
• from – from
• to – to
• targetScanDB – targetScanDB
• miRNAPromoterScoreThreshold – miRNAPromoterScoreThreshold
• targetGenePromoterScoreThreshold – targetGenePromoterScoreThreshold
• miRNATargetScoreThreshold – miRNATargetScoreThreshold
• scoreThreshold – scoreThreshold
• outTable – outTable