Modules regulated by SMAD3

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

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Genes regulated by SMAD3

Genes likely regulated by SMAD3 through linked binding evidence in open chromatin. The chart ranks TF-linked genes by their mean Perturb-seq response to SMAD3 knockdown, with negative coefficients indicating downregulation and positive coefficients indicating upregulation upon knockdown.

TFs regulating SMAD3 0 TFs

Transcription factors with Perturb-seq knockdown data for SMAD3. 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 = SMAD3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

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Elements linked to SMAD3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of SMAD3, 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.

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Genome Browser

Genomic view of the SMAD3 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.