This gene encodes a member of the AT-rich interactive domain (ARID)-containing family of DNA-binding proteins. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and chromatin structure modification. This protein functions as a subunit of the polybromo- and BRG1-associated factor or PBAF (SWI/SNF-B) chromatin remodeling complex which facilitates ligand-dependent transcriptional activation by nuclear receptors. Mutations in this gene are associated with hepatocellular carcinomas. A pseudogene of this gene is found on chromosome1. [provided by RefSeq, Dec 2016]
Modules significantly affected by knockdown. ↑ Up = module upregulated upon KD; ↓ Down = module downregulated upon KD.
| Cluster | Dir | NES | padj | Bind | OR | padj (bind) |
|---|
| Module | Dir | NES | #gRNA | padj | Bind | OR | padj (bind) |
|---|
| Submodule | Module | Dir | NES | #gRNA | Bind | OR | padj (bind) |
|---|
Genes likely regulated by ARID2 through linked binding evidence in open chromatin. The chart ranks TF-linked genes by their mean Perturb-seq response to ARID2 knockdown, with negative coefficients indicating downregulation and positive coefficients indicating upregulation upon knockdown.
Open chromatin elements (ATAC-seq) where ARID2 has ChIP-seq or motif footprint binding evidence and which are linked to at least one target gene region.
| Element | Size | Linked genes |
|---|
Transcription factors with Perturb-seq knockdown data for ARID2. 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 = ARID2 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of ARID2, 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.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr12:45,546,741–45,547,764 | 182.4 kb | Distal (>10kb) Multiome HiCAR | 87 | |
| chr12:45,725,008–45,725,200 | 4.5 kb | Proximal (<10kb) | 21 | |
| chr12:45,726,865–45,728,208 | 2.1 kb | Proximal (<10kb) Multiome | 991 | |
| chr12:45,728,446–45,731,126 | 690 bp | At TSS Multiome | 1023 | |
| chr12:45,989,594–45,992,639 | 261.0 kb | Distal (>10kb) Multiome | 1242 |
Genomic view of the ARID2 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.