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eRNAs quantification


A total of ~300k eRNAs were firstly included in the TCeA. The expression level (RPKM) of these super-enhancer eRNAs in TCGA, GTEx, and CCLE samples can be downloaded below.

Since the initial systematic annotation of Super-enhancers (Hnisz et al., 2013), more and more H3K27ac profiles in diverse cell/tissue types have been aggregated. To further explore the regulatory genome, we collected a bundle of ~350 H3K27ac profiles from cistrome (Liu et al., 2011) and SEdb (Jiang et al., 2019) and annotated an additional ~320Mb putative super-enhancer regions using the ROSE software (Whyte et al., 2013). The PCA model derived in the initial analysis was applied on these putative super-enhancer regions. Another ~200k eRNA loci were discovered in these regions. The expression level (RPKM) of these putative super-enhancer eRNAs cound be obtained below too.

Besides these, the expression level (RPKM) of ~63k FANTOM CAGE-based eRNAs is also provided. This is an updated dataset of our previous publication, adding GTEx and CCLE samples Chen et al 2018.


Dataset eRNAs in ENCODE
super-enhancers
(n=~300k)		 eRNAs in putative
super-enhancers
(n=~200k)		 eRNAs from
typical enhancers
(n=~63k)
All TCGA samples 8.6 Gb 5.2 Gb 1.2 Gb
All GTEx samples 6.0 Gb 3.2 Gb 928 Mb
All CCLE samples 772 Mb 315 Mb 139 Mb







The expression level (RPKM) of super-enhancer eRNAs by individual TCGA cancer type or GTEx tissue type can be obtained below separately.


Dataset eRNAs in ENCODE
super-enhancers
(n=~300k)		 eRNAs in putative
super-enhancers
(n=~200k)		 eRNAs from
typical enhancers
(n=~63k)
TCGA-ACC 45 Mb 28 Mb 7.4 Mb
TCGA-BLCA 343 Mb 204 Mb 150 Mb
TCGA-BRCA 1.2 Gb 732 Mb 23 Mb
TCGA-CESC 253 Mb 150 Mb 36 Mb
TCGA-CHOL 33 Mb 20 Mb 5.3 Mb
TCGA-COAD/READ 355 Mb 207 Mb 47 Mb
TCGA-DLBC 30 Mb 27 Mb 6.1 Mb
TCGA-ESCA 262 Mb 156 Mb 46 Mb
TCGA-GBM 114 Mb 66 Mb 18 Mb
TCGA-HNSC 420 Mb 252 Mb 62 Mb
TCGA-KICH 68 Mb 41 Mb 11 Mb
TCGA-KIRC 525 Mb 314 Mb 81 Mb
TCGA-KIRP 263 Mb 159 Mb 38 Mb
TCGA-LAML 46 Mb 27 Mb 7.7 Mb
TCGA-LGG 469 Mb 294 Mb 69 Mb
TCGA-LIHC 299 Mb 143 Mb 32 Mb
TCGA-LUAD 547 Mb 322 Mb 75 Mb
TCGA-LUSC 532 Mb 319 Mb 74 Mb
TCGA-MESO 63 Mb 36 Mb 10 Mb
TCGA-OV 306 Mb 177 Mb 50 Mb
TCGA-PAAD 155 Mb 87 Mb 23 Mb
TCGA-PCPG 120 Mb 75 Mb 19 Mb
TCGA-PRAD 455 Mb 277 Mb 49 Mb
TCGA-SARC 181 Mb 107 Mb 16 Mb
TCGA-SKCM 276 Mb 166 Mb 23 Mb
TCGA-STAD 551 Mb 322 Mb 97 Mb
TCGA-TGCT 113 Mb 72 Mb 18 Mb
TCGA-THCA 511 Mb 307 Mb 67 Mb
TCGA-THYM 91 Mb 55 Mb 14 Mb
TCGA-UCEC 138 Mb 85 Mb 14 Mb
TCGA-UCS 38 Mb 24 Mb 6.6 Mb
TCGA-UVM 39 Mb 23 Mb 5.9 Mb





GTEx tissue type eRNAs in ENCODE
super-enhancers
(n=~300k)		 eRNAs in putative
super-enhancers
(n=~200k)		 eRNAs from
typical enhancers
(n=~63k)
Adipose Tissue 444 Mb 234 Mb 64 Mb
Adrenal Gland 126 Mb 67 Mb 18 Mb
Bladder 8.4 Mb 4.6 Mb 1.9 Mb
Blood 338 Mb 159 Mb 53 Mb
Blood_Vessel 432 Mb 228 Mb 61 Mb
Brain 285 Mb 171 Mb 53 Mb
Breast 201 Mb 106 Mb 30 Mb
Cervix_Uteri 8.0 Mb 4.5 Mb 1.8 Mb
Colon 274 Mb 144 Mb 39 Mb
Esophagus 445 Mb 238 Mb 63 Mb
Fallopian Tube 6.5 Mb 3.6 Mb 1.6 Mb
Heart 275 Mb 142 Mb 40 Mb
Kidney 28 Mb 15 Mb 4.8 Mb
Liver 90 Mb 49 Mb 14 Mb
Lung 346 Mb 178 Mb 52 Mb
Muscle 276 Mb 140 Mb 39 Mb
Nerve 322 Mb 174 Mb 48 Mb
Ovary 99 Mb 55 Mb 16 Mb
Pancreas 142 Mb 77 Mb 20 Mb
Pituitary 114 Mb 64 Mb 19 Mb
Prostate 113 Mb 60 Mb 17 Mb
Salivary Gland 64 Mb 34 Mb 10 Mb
Skin 576 Mb 318 Mb 85 Mb
Small Intestine 100 Mb 51 Mb 16 Mb
Spleen 109 Mb 54 Mb 17 Mb
Stomach 162 Mb 84 Mb 23 Mb
Testis 199 Mb 118 Mb 43 Mb
Thyroid 350 Mb 191 Mb 51 Mb
Uterus 82 Mb 44 Mb 13 Mb
Vagina 90 Mb 48 Mb 14 Mb