PDCD4
programmed cell death 4 | H731

This gene is a tumor suppressor and encodes a protein that binds to the eukaryotic translation initiation factor 4A1 and inhibits its function by preventing RNA binding. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]

Member of: DE-8 DE-8.15 Developmental clusters: GC6
Biological processes 29 terms
BMP signaling pathway (GO:0030509)apoptotic process (GO:0006915)cellular response to lipopolysaccharide (GO:0071222)cellular response to lipopolysaccharide (GO:0071222)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)cytosol (GO:0005829)epithelial to mesenchymal transition involved in cardiac fibroblast development (GO:0060940)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of JUN kinase activity (GO:0043508)negative regulation of cytokine production involved in inflammatory response (GO:1900016)negative regulation of cytokine production involved in inflammatory response (GO:1900016)negative regulation of myofibroblast differentiation (GO:1904761)negative regulation of vascular associated smooth muscle cell differentiation (GO:1905064)negative regulation of vascular associated smooth muscle cell proliferation (GO:1904706)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of endothelial cell apoptotic process (GO:2000353)positive regulation of inflammatory response (GO:0050729)positive regulation of inflammatory response (GO:0050729)positive regulation of non-canonical NF-kappaB signal transduction (GO:1901224)positive regulation of vascular associated smooth muscle cell apoptotic process (GO:1905461)protein binding (GO:0005515)
Expression (TPM)
PDCD4 — as a Regulated Gene

TFs regulating PDCD4 0 TFs

Transcription factors with Perturb-seq knockdown data for PDCD4. 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 = PDCD4 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to PDCD4

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of PDCD4, 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
chr10:110,610,178–110,611,174 261.3 kb Distal (>10kb) Multiome 383
chr10:110,643,641–110,644,831 227.6 kb Distal (>10kb) Multiome 427
chr10:110,671,928–110,672,573 199.6 kb Distal (>10kb) Multiome 567
chr10:110,701,236–110,702,762 170.0 kb Distal (>10kb) Multiome 253
chr10:110,833,606–110,834,169 38.1 kb Distal (>10kb) Multiome 160
chr10:110,857,173–110,858,770 14.3 kb Distal (>10kb) Multiome 690
chr10:110,871,026–110,872,969 60 bp At TSS Multiome 918
chr10:110,918,245–110,920,897 47.5 kb Distal (>10kb) Multiome 1037
chr10:111,075,793–111,079,438 204.5 kb Distal (>10kb) Multiome 555
chr10:111,136,785–111,137,423 265.2 kb Distal (>10kb) Multiome 188

Genome Browser

Genomic view of the PDCD4 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.

chr10:110,600,178 – 111,147,423
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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