sydSeq

sydSeq analyzes regulatory relationships between micro-RNAs (miRNAs) and messenger RNAs (mRNAs) using a supervised significance-combination framework (pMim) to identify differentially expressed miRNAs and evaluate pathway-level impacts on predicted target mRNAs.

Key Features:

• Implementation: Implemented as an R package with a central pMim function for supervised miRNA–mRNA interaction analysis.
• Supervised significance-combination framework: Uses significance-combination concepts to jointly rank regulatory miRNAs and their potential functional impacts.
• Differential expression testing: Tests miRNA differential expression and assesses whether predicted target mRNAs in shared pathways change in the opposite direction.
• Database integration: Integrates existing miRNA target and pathway databases for annotation and to stabilize estimation in small sample sizes.
• Interpretability and concordance: Produces interpretable results reported to be more concordant with established literature than simpler approaches.

Scientific Applications:

• miRNA–mRNA regulatory analysis: Identification and ranking of putative regulatory miRNAs and their mRNA targets in gene regulation studies.
• Small-sample studies: Analysis of datasets with limited sample sizes, such as rare disease investigations or preliminary exploratory studies.
• Pathway-level interpretation: Contextualization of miRNA–mRNA interactions within biological pathways to infer potential functional impacts.

Methodology:

Combines statistical differential expression testing with significance-combination concepts in pMim and annotates results using miRNA target and pathway databases to jointly assess miRNA expression and predicted target mRNA changes at the pathway level.