Modules regulated by SMAD4

Modules significantly affected by knockdown. ↑ Up = module upregulated upon KD; ↓ Down = module downregulated upon KD.

---

Genes regulated by SMAD4

Genes likely regulated by SMAD4 through linked binding evidence in open chromatin. The chart ranks TF-linked genes by their mean Perturb-seq response to SMAD4 knockdown, with negative coefficients indicating downregulation and positive coefficients indicating upregulation upon knockdown.

TFs regulating SMAD4 0 TFs

Transcription factors with Perturb-seq knockdown data for SMAD4. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = SMAD4 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

---

Elements linked to SMAD4

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of SMAD4, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

---

Genome Browser

Genomic view of the SMAD4 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.