An improved version of PrESSTo, called SlideBase is now available at http://slidebase.binf.ku.dk
SlideBase offers selection of cell or tissue specific genomic elements using sliders for the following datasets:

Predefined enhancer data.

Using statistical methods, we have defined several enhancer tracks used in Andersson et al. Most track sets are defined in the BED format unless specified otherwise and can be downloaded. Tracks from section 1 to 3 can also be viewed in the UCSC Genome Browser Each predicted enhancer is described in BED12 format with two blocks denoting the merged regions of transcription initiation on the minus and plus strands. The thickStart and thickEnd columns denote the inferred mid position. The score column gives the maximum pooled expression of TCs used to construct each bidirectional loci.

Download/View

NameDownload LinkUCSC Genome Browser Link
ubiquitous enhancers (cells)Ubiquitous_enhancers_S9.bedubiquitous enhancers (cells)
ubiquitous enhancers (organs)Ubiquitous_enhancers_S10.bedubiquitous enhancers (organs)
tss-enhancer associationsenhancer_tss_associations.bedtss-enhancer associations
permissive enhancerspermissive_enhancers.bed permissive enhancers
robust enhancersrobust_enhancers.bedrobust enhancers

Download/View

Cell NameDownload LinkUCSC Genome Browser Link
acinar cellCL:0000622_acinar_cell_differentially_expressed_enhancers.bedacinar cell
amniotic epithelial cellCL:0002536_amniotic_epithelial_cell_differentially_expressed_enhancers.bedamniotic epithelial cell
astrocyteCL:0000127_astrocyte_differentially_expressed_enhancers.bedastrocyte
basophilCL:0000767_basophil_differentially_expressed_enhancers.bedbasophil
blood vessel endothelial cellCL:0000071_blood_vessel_endothelial_cell_differentially_expressed_enhancers.bedblood vessel endothelial cell
bronchial smooth muscle cellCL:0002598_bronchial_smooth_muscle_cell_differentially_expressed_enhancers.bedbronchial smooth muscle cell
cardiac fibroblastCL:0002548_cardiac_fibroblast_differentially_expressed_enhancers.bedcardiac fibroblast
cardiac myocyteCL:0000746_cardiac_myocyte_differentially_expressed_enhancers.bedcardiac myocyte
chondrocyteCL:0000138_chondrocyte_differentially_expressed_enhancers.bedchondrocyte
ciliated epithelial cellCL:0000067_ciliated_epithelial_cell_differentially_expressed_enhancers.bedciliated epithelial cell
corneal epithelial cellCL:0000575_corneal_epithelial_cell_differentially_expressed_enhancers.bedcorneal epithelial cell
dendritic cellCL:0000451_dendritic_cell_differentially_expressed_enhancers.beddendritic cell
endothelial cell of hepatic sinusoidCL:1000398_endothelial_cell_of_hepatic_sinusoid_differentially_expressed_enhancers.bedendothelial cell of hepatic sinusoid
endothelial cell of lymphatic vesselCL:0002138_endothelial_cell_of_lymphatic_vessel_differentially_expressed_enhancers.bedendothelial cell of lymphatic vessel
enteric smooth muscle cellCL:0002504_enteric_smooth_muscle_cell_differentially_expressed_enhancers.bedenteric smooth muscle cell
epithelial cell of esophagusCL:0002252_epithelial_cell_of_esophagus_differentially_expressed_enhancers.bedepithelial cell of esophagus
epithelial cell of MalassezCL:0002166_epithelial_cell_of_Malassez_differentially_expressed_enhancers.bedepithelial cell of Malassez
epithelial cell of prostateCL:0002231_epithelial_cell_of_prostate_differentially_expressed_enhancers.bedepithelial cell of prostate
fat cellCL:0000136_fat_cell_differentially_expressed_enhancers.bedfat cell
fibroblast of choroid plexusCL:0002549_fibroblast_of_choroid_plexus_differentially_expressed_enhancers.bedfibroblast of choroid plexus
fibroblast of gingivaCL:0002552_fibroblast_of_gingiva_differentially_expressed_enhancers.bedfibroblast of gingiva
fibroblast of lymphatic vesselCL:0002554_fibroblast_of_lymphatic_vessel_differentially_expressed_enhancers.bedfibroblast of lymphatic vessel
fibroblast of periodontiumCL:0002556_fibroblast_of_periodontium_differentially_expressed_enhancers.bedfibroblast of periodontium
fibroblast of pulmonary arteryCL:0002557_fibroblast_of_pulmonary_artery_differentially_expressed_enhancers.bedfibroblast of pulmonary artery
fibroblast of the conjuctivaCL:0002550_fibroblast_of_the_conjuctiva_differentially_expressed_enhancers.bedfibroblast of the conjuctiva
fibroblast of tunica adventitia of arteryCL:1000306_fibroblast_of_tunica_adventitia_of_artery_differentially_expressed_enhancers.bedfibroblast of tunica adventitia of artery
gingival epithelial cellCL:0002621_gingival_epithelial_cell_differentially_expressed_enhancers.bedgingival epithelial cell
hair follicle cellCL:0002559_hair_follicle_cell_differentially_expressed_enhancers.bedhair follicle cell
hepatic stellate cellCL:0000632_hepatic_stellate_cell_differentially_expressed_enhancers.bedhepatic stellate cell
hepatocyteCL:0000182_hepatocyte_differentially_expressed_enhancers.bedhepatocyte
intestinal epithelial cellCL:0002563_intestinal_epithelial_cell_differentially_expressed_enhancers.bedintestinal epithelial cell
iris pigment epithelial cellCL:0002565_iris_pigment_epithelial_cell_differentially_expressed_enhancers.bediris pigment epithelial cell
keratinocyteCL:0000312_keratinocyte_differentially_expressed_enhancers.bedkeratinocyte
keratocyteCL:0002363_keratocyte_differentially_expressed_enhancers.bedkeratocyte
kidney epithelial cellCL:0002518_kidney_epithelial_cell_differentially_expressed_enhancers.bedkidney epithelial cell
lens epithelial cellCL:0002224_lens_epithelial_cell_differentially_expressed_enhancers.bedlens epithelial cell
lymphocyte of B lineageCL:0000945_lymphocyte_of_B_lineage_differentially_expressed_enhancers.bedlymphocyte of B lineage
macrophageCL:0000235_macrophage_differentially_expressed_enhancers.bedmacrophage
mammary epithelial cellCL:0002327_mammary_epithelial_cell_differentially_expressed_enhancers.bedmammary epithelial cell
mast cellCL:0000097_mast_cell_differentially_expressed_enhancers.bedmast cell
melanocyteCL:0000148_melanocyte_differentially_expressed_enhancers.bedmelanocyte
mesenchymal cellCL:0000134_mesenchymal_cell_differentially_expressed_enhancers.bedmesenchymal cell
mesothelial cellCL:0000077_mesothelial_cell_differentially_expressed_enhancers.bedmesothelial cell
monocyteCL:0000576_monocyte_differentially_expressed_enhancers.bedmonocyte
myoblastCL:0000056_myoblast_differentially_expressed_enhancers.bedmyoblast
natural killer cellCL:0000623_natural_killer_cell_differentially_expressed_enhancers.bednatural killer cell
neuronCL:0000540_neuron_differentially_expressed_enhancers.bedneuron
neuronal stem cellCL:0000047_neuronal_stem_cell_differentially_expressed_enhancers.bedneuronal stem cell
neutrophilCL:0000775_neutrophil_differentially_expressed_enhancers.bedneutrophil
osteoblastCL:0000062_osteoblast_differentially_expressed_enhancers.bedosteoblast
pericyte cellCL:0000669_pericyte_cell_differentially_expressed_enhancers.bedpericyte cell
placental epithelial cellCL:0002577_placental_epithelial_cell_differentially_expressed_enhancers.bedplacental epithelial cell
preadipocyteCL:0002334_preadipocyte_differentially_expressed_enhancers.bedpreadipocyte
respiratory epithelial cellCL:0002368_respiratory_epithelial_cell_differentially_expressed_enhancers.bedrespiratory epithelial cell
reticulocyteCL:0000558_reticulocyte_differentially_expressed_enhancers.bedreticulocyte
retinal pigment epithelial cellCL:0002586_retinal_pigment_epithelial_cell_differentially_expressed_enhancers.bedretinal pigment epithelial cell
sensory epithelial cellCL:0000098_sensory_epithelial_cell_differentially_expressed_enhancers.bedsensory epithelial cell
skeletal muscle cellCL:0000188_skeletal_muscle_cell_differentially_expressed_enhancers.bedskeletal muscle cell
skin fibroblastCL:0002620_skin_fibroblast_differentially_expressed_enhancers.bedskin fibroblast
smooth muscle cell of prostateCL:1000487_smooth_muscle_cell_of_prostate_differentially_expressed_enhancers.bedsmooth muscle cell of prostate
smooth muscle cell of the esophagusCL:0002599_smooth_muscle_cell_of_the_esophagus_differentially_expressed_enhancers.bedsmooth muscle cell of the esophagus
smooth muscle cell of tracheaCL:0002600_smooth_muscle_cell_of_trachea_differentially_expressed_enhancers.bedsmooth muscle cell of trachea
stromal cellCL:0000499_stromal_cell_differentially_expressed_enhancers.bedstromal cell
tendon cellCL:0000388_tendon_cell_differentially_expressed_enhancers.bedtendon cell
trabecular meshwork cellCL:0002367_trabecular_meshwork_cell_differentially_expressed_enhancers.bedtrabecular meshwork cell
T cellCL:0000084_T_cell_differentially_expressed_enhancers.bedT cell
urothelial cellCL:0000731_urothelial_cell_differentially_expressed_enhancers.bedurothelial cell
uterine smooth muscle cellCL:0002601_uterine_smooth_muscle_cell_differentially_expressed_enhancers.beduterine smooth muscle cell
vascular associated smooth muscle cellCL:0000359_vascular_associated_smooth_muscle_cell_differentially_expressed_enhancers.bedvascular associated smooth muscle cell

Download/View

Organ NameDownload LinkUCSC Genome Browser Link
adipose tissueUBERON:0001013_adipose_tissue_differentially_expressed_enhancers.bedadipose tissue
bloodUBERON:0000178_blood_differentially_expressed_enhancers.bedblood
blood vesselUBERON:0001981_blood_vessel_differentially_expressed_enhancers.bedblood vessel
brainUBERON:0000955_brain_differentially_expressed_enhancers.bedbrain
esophagusUBERON:0001043_esophagus_differentially_expressed_enhancers.bedesophagus
eyeUBERON:0000970_eye_differentially_expressed_enhancers.bedeye
female gonadUBERON:0000992_female_gonad_differentially_expressed_enhancers.bedfemale gonad
gallbladderUBERON:0002110_gallbladder_differentially_expressed_enhancers.bedgallbladder
heartUBERON:0000948_heart_differentially_expressed_enhancers.bedheart
internal male genitaliaUBERON:0004054_internal_male_genitalia_differentially_expressed_enhancers.bedinternal male genitalia
kidneyUBERON:0002113_kidney_differentially_expressed_enhancers.bedkidney
large intestineUBERON:0000059_large_intestine_differentially_expressed_enhancers.bedlarge intestine
liverUBERON:0002107_liver_differentially_expressed_enhancers.bedliver
lungUBERON:0002048_lung_differentially_expressed_enhancers.bedlung
lymph nodeUBERON:0000029_lymph_node_differentially_expressed_enhancers.bedlymph node
meninxUBERON:0002360_meninx_differentially_expressed_enhancers.bedmeninx
olfactory regionUBERON:0003112_olfactory_region_differentially_expressed_enhancers.bedolfactory region
pancreasUBERON:0001264_pancreas_differentially_expressed_enhancers.bedpancreas
parotid glandUBERON:0001831_parotid_gland_differentially_expressed_enhancers.bedparotid gland
penisUBERON:0000989_penis_differentially_expressed_enhancers.bedpenis
placentaUBERON:0001987_placenta_differentially_expressed_enhancers.bedplacenta
prostate glandUBERON:0002367_prostate_gland_differentially_expressed_enhancers.bedprostate gland
salivary glandUBERON:0001044_salivary_gland_differentially_expressed_enhancers.bedsalivary gland
skeletal muscle tissueUBERON:0001134_skeletal_muscle_tissue_differentially_expressed_enhancers.bedskeletal muscle tissue
skin of bodyUBERON:0002097_skin_of_body_differentially_expressed_enhancers.bedskin of body
small intestineUBERON:0002108_small_intestine_differentially_expressed_enhancers.bedsmall intestine
smooth muscle tissueUBERON:0001135_smooth_muscle_tissue_differentially_expressed_enhancers.bedsmooth muscle tissue
spinal cordUBERON:0002240_spinal_cord_differentially_expressed_enhancers.bedspinal cord
spleenUBERON:0002106_spleen_differentially_expressed_enhancers.bedspleen
stomachUBERON:0000945_stomach_differentially_expressed_enhancers.bedstomach
submandibular glandUBERON:0001736_submandibular_gland_differentially_expressed_enhancers.bedsubmandibular gland
testisUBERON:0000473_testis_differentially_expressed_enhancers.bedtestis
throatUBERON:0000341_throat_differentially_expressed_enhancers.bedthroat
thymusUBERON:0002370_thymus_differentially_expressed_enhancers.bedthymus
thyroid glandUBERON:0002046_thyroid_gland_differentially_expressed_enhancers.bedthyroid gland
tongueUBERON:0001723_tongue_differentially_expressed_enhancers.bedtongue
tonsilUBERON:0002372_tonsil_differentially_expressed_enhancers.bedtonsil
umbilical cordUBERON:0002331_umbilical_cord_differentially_expressed_enhancers.bedumbilical cord
urinary bladderUBERON:0001255_urinary_bladder_differentially_expressed_enhancers.bedurinary bladder
uterusUBERON:0000995_uterus_differentially_expressed_enhancers.beduterus
vaginaUBERON:0000996_vagina_differentially_expressed_enhancers.bedvagina

Download or View Tracks

Download the selected enhancer sets (from sections 1, 2 and 3) above as one BED file

View the selected enhancer sets (from sections 1, 2 and 3) above in UCSC Genome Browser

4. Enhancer Expression

Download expressed enhancers in all facets

Download enhancers that are positively differentially expressed in each facet against any other facet

Binary matrix of enhancer usage (significant enhancer expression compared to random regions, 1 means used) across all considered FANTOM libraries:
Download Usage file

Expression (TPM and RLE normalized) matrix of enhancers across all considered FANTOM libraries:
Download Expression file

5. Enhancer - FANTOM Robust Promoter associations

Download Enhancer-Promoter Cell Type Associations

Download Enhancer-Promoter Organ Associations

Note:Enhancer - Promoter associations are obtained by correlating enhancer-promoter pairs within 500 kbases over cell type and organ facets and filtered by an adjusted correlation pvalue: FDR < 10-5
The enhancer-promoter associations are computed between enhancers and all FANTOM robust promoters. For enhancer-RefSeq promoter associations click here

Download enhancer-promoter associations made for DPI clusters