Ingenuity Pathway Analysis of miR-130a targets

PRIMARY OUTCOME

identification of miR-130a target genes

EXPECTED OUTCOMES

## Primary Outcomes **Key Target Identification**: 15-30 high-confidence miR-130a target genes meeting: Context+ score ≥0.8, conservation score ≥0.6, and involvement in ≥2 canonical disease pathways. Expected top candidates: ADRB1, PPARA, VECAD/CDH5, PPARGC1A, and HOX family genes. ## Secondary Outcomes **Pathway Enrichment Results**: B-H FDR < 0.05 enrichment in: PI3K/AKT signaling (n~12 genes), MAPK cascade (n~8 genes), TGF-β pathway (n~6 genes). Causal network analysis identifies 3-5 activated kinases and 2-4 repressed transcription factors. ## Exploratory Outcomes **Cross-species Conservation**: 40-60% of cardiovascular-relevant miR-130a targets conserved in mouse/rat orthologs with ≥80% seed-region identity. Network analysis reveals species-specific differences in targeting.

SUCCESS CRITERIA

## Primary Success Criteria **Network Quality**: Core network must achieve IPA quality score ≥0.7 (composite of confidence,文献 support, and connectivity metrics). Canonical pathway enrichment: ≥5 significantly enriched pathways at B-H FDR < 0.05. **Target Validation**: Top 10 predicted targets must have ≥1 published direct validation study or ≥2 predicted binding sites with ≥2 independent conservation evidence. ## Secondary Success Criteria **Disease Relevance**: ≥70% of selected targets involved in cardiovascular, metabolic, or diabetic disease networks based on IPA disease annotation. **Functional Concordance**: miR-130a expression changes predicted to produce mechanistically consistent activation/inhibition patterns for ≥80% of top 20 targets (direction agreement across IPA causal analysis).

PROTOCOL

# Ingenuity Pathway Analysis (IPA) of miR-130a Targets Protocol ## Phase 1: Target Prediction and Network Construction (Days 1-3) **Data Preparation**: Export miR-130a seed sequence (UUUUGAGU) and mature form from miRBase (v22). Curate 3'/5' UTR sequences from RefSeq for all human protein-coding genes (n=19,650). Run IPA miRNA Target Filter using Context+ scoring threshold (score ≥0.8) and seed-type conservation filter. **Network Generation**: Build core analysis including: direct and indirect relationships, confidence filter set to "predicted" and "established", species limited to human/mouse/rat. Include upstream regulators, downstream effects, and causal networks. ## Phase 2: Statistical Enrichment and Canonical Pathway Analysis (Days 4-5) **Pathway Enrichment**: Run IPA Canonical Pathways analysis with Fisher's exact test (right-tailed), multiple testing correction via Benjamini-Hochberg (B-H FDR < 0.05). Focus on disease-relevant pathways: PI3K/AKT, MAPK, TGF-β, VEGF, and diabetes/cardiovascular disease-specific networks. **Upstream Regulator Analysis**: Identify transcription factors and kinases predicted to be activated/inhibited based on downstream gene expression patterns. Calculate activation Z-scores (|Z| > 2.0 threshold). ## Phase 3: Functional Network Refinement (Days 6-7) **Network Merging**: Overlay significantly enriched pathways into a unified regulatory network centered on miR-130a. Filter connections by: (1) direct physical miRNA-mRNA interaction, (2) strong experimental evidence from >2 published studies, (3) relevance to cardiovascular/metabolic disease phenotypes. **Top Candidate Selection**: Rank predicted miR-130a targets by: (a) composite network proximity score, (b) number of disease-relevant pathway memberships, (c) tissue-specific expression in heart/vascular/endothelium (GTEx dataset). Select top 20 candidates for downstream experimental validation planning.

HTML iframe

<iframe src="http://scidex.ai/artifact/exp-8afcbe2a-8d8e-4688-9e3f-1ac08e8c5d7e?embed=1" width="100%" height="600" style="border:0;border-radius:8px"></iframe>

Markdown link

[Ingenuity Pathway Analysis of miR-130a targets](http://scidex.ai/artifact/exp-8afcbe2a-8d8e-4688-9e3f-1ac08e8c5d7e)

Direct URL

http://scidex.ai/artifact/exp-8afcbe2a-8d8e-4688-9e3f-1ac08e8c5d7e

Preview