This site contains collections of sequence motifs enriched in human bidirectional CAGE enhancers as described in Andersen et al. 2014, Nature. The underlying CAGE data was produced at the RIKEN OSC as part of the international FANTOM consortium and is described in Forrest et al. 2014, Nature.

Sequence motifs were extracted from enhancers or promoters (either all or those showing differential activity in primary cells or tissues) using HOMER, a suite of tools for motif discovery and next-gen sequencing analysis developed by Christopher Benner (Integrative Genomics Core, Salk Institute, San Diego).

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• Description of results

Motif collections for complete enhancer/promoter sets

• Bidirectional CAGE-enhancers (known motifs) (de novo motifs)
• CAGE-TSS associated with CpG islands (known motifs) (de novo motifs)
• CAGE-TSS not associated with CpG islands (known motifs) (de novo motifs)
• CAGE-TSS associated with CpG islands (known promoters) (known motifs) (de novo motifs)
• CAGE-TSS not associated with CpG islands (known promoters) (known motifs) (de novo motifs)

Motif collections for cell type-specific enhancer sets

• acinar cell (known motifs) (de novo motifs)
• amniotic epithelial cell (known motifs) (de novo motifs)
• astrocyte (known motifs) (de novo motifs)
• basophil (known motifs) (de novo motifs)
• blood vessel endothelial cell (known motifs) (de novo motifs)
• bronchial smooth muscle cell (known motifs) (de novo motifs)
• cardiac fibroblast (known motifs) (de novo motifs)
• cardiac myocyte (known motifs) (de novo motifs)
• chondrocyte (known motifs) (de novo motifs)
• ciliated epithelial cell (known motifs) (de novo motifs)
• circulating cell (known motifs) (de novo motifs)
• corneal epithelial cell (known motifs) (de novo motifs)
• dendritic cell (known motifs) (de novo motifs)
• endothelial cell of hepatic sinusoid (known motifs) (de novo motifs)
• endothelial cell of lymphatic vessel (known motifs) (de novo motifs)
• enteric smooth muscle cell (known motifs) (de novo motifs)
• epithelial cell of esophagus (known motifs) (de novo motifs)
• epithelial cell of Malassez (known motifs) (de novo motifs)
• epithelial cell of prostate (known motifs) (de novo motifs)
• fat cell (known motifs) (de novo motifs)
• fibroblast of choroid plexus (known motifs) (de novo motifs)
• fibroblast of gingiva (known motifs) (de novo motifs)
• fibroblast of lymphatic vessel (known motifs) (de novo motifs)
• fibroblast of periodontium (known motifs) (de novo motifs)
• fibroblast of pulmonary artery (known motifs) (de novo motifs)
• fibroblast of the conjuctiva (known motifs) (de novo motifs)
• fibroblast of tunica adventitia of artery (known motifs) (de novo motifs)
• gingival epithelial cell (known motifs) (de novo motifs)
• granulocyte (known motifs) (de novo motifs)
• hair follicle cell (known motifs) (de novo motifs)
• hepatic stellate cell (known motifs) (de novo motifs)
• hepatocyte (known motifs) (de novo motifs)
• intestinal epithelial cell (known motifs) (no de novo motifs)
• iris pigment epithelial cell (known motifs) (de novo motifs)
• keratinocyte (known motifs) (de novo motifs)
• keratocyte (known motifs) (de novo motifs)
• kidney epithelial cell (known motifs) (de novo motifs)
• lens epithelial cell (known motifs) (de novo motifs)
• lymphocyte of B lineage (known motifs) (de novo motifs)
• macrophage (known motifs) (de novo motifs)
• mammary epithelial cell (known motifs) (de novo motifs)
• mast cell (known motifs) (de novo motifs)
• melanocyte (known motifs) (de novo motifs)
• mesenchymal cell (known motifs) (de novo motifs)
• mesothelial cell (known motifs) (de novo motifs)
• monocyte (known motifs) (de novo motifs)
• myoblast (known motifs) (de novo motifs)
• natural killer cell (known motifs) (de novo motifs)
• neuron (known motifs) (de novo motifs)
• neuronal stem cell (known motifs) (de novo motifs)
• neutrophil (known motifs) (de novo motifs)
• osteoblast (known motifs) (de novo motifs)
• pericyte cell (known motifs) (de novo motifs)
• placental epithelial cell (known motifs) (de novo motifs)
• preadipocyte (known motifs) (de novo motifs)
• respiratory epithelial cell (known motifs) (de novo motifs)
• reticulocyte (known motifs) (de novo motifs)
• retinal pigment epithelial cell (known motifs) (de novo motifs)
• sensory epithelial cell (known motifs) (de novo motifs)
• skeletal muscle cell (known motifs) (de novo motifs)
• skin fibroblast (known motifs) (de novo motifs)
• smooth muscle cell of prostate (known motifs) (de novo motifs)
• smooth muscle cell of the esophagus (known motifs) (no de novo motifs)
• smooth muscle cell of trachea (known motifs) (de novo motifs)
• stromal cell (known motifs) (de novo motifs)
• T cell (known motifs) (de novo motifs)
• tendon cell (known motifs) (de novo motifs)
• trabecular meshwork cell (known motifs) (de novo motifs)
• urothelial cell (known motifs) (de novo motifs)
• uterine smooth muscle cell (known motifs) (de novo motifs)
• vascular associated smooth muscle cell (known motifs) (de novo motifs)

Motif collections for tissue-specific enhancer sets

• adipose tissue (known motifs) (no de novo motifs)
• blood (known motifs) (de novo motifs)
• blood vessel (known motifs) (no de novo motifs)
• brain (known motifs) (de novo motifs)
• esophagus (known motifs) (de novo motifs)
• eye (known motifs) (no de novo motifs)
• female gonad (known motifs) (de novo motifs)
• gallbladder (known motifs) (no de novo motifs)
• heart (known motifs) (de novo motifs)
• internal male genitalia (known motifs) (no de novo motifs)
• kidney (known motifs) (de novo motifs)
• large intestine (known motifs) (de novo motifs)
• liver (known motifs) (no de novo motifs)
• lung (known motifs) (de novo motifs)
• lymph node (known motifs) (no de novo motifs)
• meninx (known motifs) (de novo motifs)
• olfactory region (known motifs) (no de novo motifs)
• pancreas (known motifs) (no de novo motifs)
• parotid gland (known motifs) (no de novo motifs)
• penis (known motifs) (no de novo motifs)
• placenta (known motifs) (no de novo motifs)
• prostate gland (known motifs) (no de novo motifs)
• salivary gland (known motifs) (de novo motifs)
• skeletal muscle tissue (known motifs) (no de novo motifs)
• skin of body (known motifs) (no de novo motifs)
• small intestine (known motifs) (no de novo motifs)
• smooth muscle tissue (known motifs) (de novo motifs)
• spinal cord (known motifs) (de novo motifs)
• spleen (known motifs) (de novo motifs)
• stomach (known motifs) (no de novo motifs)
• submandibular gland (known motifs) (de novo motifs)
• testis (known motifs) (de novo motifs)
• throat (known motifs) (no de novo motifs)
• thymus (known motifs) (no de novo motifs)
• thyroid gland (known motifs) (no de novo motifs)
• tongue (known motifs) (no de novo motifs)
• tonsil (known motifs) (de novo motifs)
• umbilical cord (known motifs) (de novo motifs)
• urinary bladder (known motifs) (de novo motifs)
• uterus (known motifs) (de novo motifs)
• vagina (known motifs) (no de novo motifs)