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ENCODE: ATAC-seq of different tissues during embryonic development
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CREMA is a free online tool that recognizes most
important transcription factors that change the chromatin
state across different samples.
Results for E2f1
Z-value: 2.93
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Correlations of motif activity and signal intensity at CREs associated with the motif's TFs:
This plot shows correlation between observed signal intensity of a CRE associated with the transcription factor across all samples and activity of the motif.
For each TF, only the top 5 correlated CREs are shown.
| CRE | Gene | Distance | Association probability | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|---|---|
| E2f1 | chr2_154569188_154570416 | 82 | 0.945459 | 0.79 | 5.9e-13 | Click! |
| E2f1 | chr2_154568994_154569145 | 651 | 0.553540 | 0.73 | 3.9e-10 | Click! |
| E2f1 | chr2_154577420_154577745 | 7690 | 0.105489 | -0.61 | 9.7e-07 | Click! |
| E2f1 | chr2_154568534_154568688 | 1109 | 0.339499 | 0.51 | 5.9e-05 | Click! |
| E2f1 | chr2_154568786_154568937 | 859 | 0.436317 | 0.42 | 1.3e-03 | Click! |
Showing 1 to 5 of 5 entries
Top target CREs of the motif:
| Cis Regulatory Element (CRE) | Target Score | Top associated gene | Gene Info | Distance of CRE to TSS | CRE/Gene association probability |
|---|---|---|---|---|---|
| chr13_23760830_23761749 | 20.74 |
H4c1 |
H4 clustered histone 1 |
59 |
0.86 |
| chr15_79690079_79691459 | 20.44 |
Gtpbp1 |
GTP binding protein 1 |
76 |
0.92 |
| chr15_102470670_102471447 | 16.77 |
Pcbp2 |
poly(rC) binding protein 2 |
10 |
0.95 |
| chr2_38286754_38287566 | 16.68 |
Dennd1a |
DENN/MADD domain containing 1A |
28 |
0.97 |
| chr15_98933816_98934775 | 16.22 |
Gm41396 |
predicted gene, 41396 |
30 |
0.62 |
| chr17_34586512_34587397 | 16.11 |
Notch4 |
notch 4 |
9 |
0.91 |
| chr3_14886091_14887033 | 15.53 |
Car2 |
carbonic anhydrase 2 |
77 |
0.97 |
| chr11_102316544_102317735 | 15.04 |
Ubtf |
upstream binding transcription factor, RNA polymerase I |
148 |
0.92 |
| chr5_23850355_23851323 | 14.60 |
2700038G22Rik |
RIKEN cDNA 2700038G22 gene |
238 |
0.81 |
| chr11_78065958_78066240 | 14.36 |
Mir144 |
microRNA 144 |
6906 |
0.08 |
Histogram of CRE-TSS distances for CREs targeted by :
Rank distribution of CRE target scores:
Distribution of target CREs across different genomic regions:
Network of associatons between targets according to the STRING database.
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.8 | 39.7 | GO:0006367 | transcription initiation from RNA polymerase II promoter(GO:0006367) |
| 1.5 | 35.0 | GO:0033014 | porphyrin-containing compound biosynthetic process(GO:0006779) tetrapyrrole biosynthetic process(GO:0033014) |
| 1.9 | 33.7 | GO:0061014 | positive regulation of mRNA catabolic process(GO:0061014) |
| 0.2 | 30.6 | GO:0008380 | RNA splicing(GO:0008380) |
| 1.1 | 23.7 | GO:0006376 | mRNA splice site selection(GO:0006376) |
| 3.9 | 23.6 | GO:2001269 | positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway(GO:2001269) |
| 0.4 | 22.1 | GO:0007052 | mitotic spindle organization(GO:0007052) |
| 6.7 | 20.2 | GO:1900739 | regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway(GO:1900739) positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway(GO:1900740) |
| 2.2 | 20.2 | GO:0048096 | chromatin-mediated maintenance of transcription(GO:0048096) |
| 0.9 | 19.8 | GO:0070979 | protein K11-linked ubiquitination(GO:0070979) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.3 | 288.4 | GO:0005654 | nucleoplasm(GO:0005654) |
| 0.1 | 205.7 | GO:0005634 | nucleus(GO:0005634) |
| 0.5 | 96.4 | GO:0000785 | chromatin(GO:0000785) |
| 0.5 | 46.6 | GO:0016604 | nuclear body(GO:0016604) |
| 0.8 | 44.3 | GO:0016605 | PML body(GO:0016605) |
| 0.1 | 39.8 | GO:0031981 | nuclear lumen(GO:0031981) |
| 0.7 | 39.1 | GO:0017053 | transcriptional repressor complex(GO:0017053) |
| 2.7 | 37.2 | GO:0035098 | ESC/E(Z) complex(GO:0035098) |
| 0.4 | 36.6 | GO:0005681 | spliceosomal complex(GO:0005681) |
| 1.2 | 35.9 | GO:0010494 | cytoplasmic stress granule(GO:0010494) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 111.4 | GO:0044822 | poly(A) RNA binding(GO:0044822) |
| 0.4 | 46.7 | GO:0061630 | ubiquitin protein ligase activity(GO:0061630) |
| 0.2 | 41.3 | GO:0004674 | protein serine/threonine kinase activity(GO:0004674) |
| 0.2 | 38.0 | GO:0003682 | chromatin binding(GO:0003682) |
| 0.9 | 32.7 | GO:0004402 | histone acetyltransferase activity(GO:0004402) |
| 1.0 | 27.3 | GO:0001205 | transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding(GO:0001205) |
| 2.1 | 26.7 | GO:0070577 | lysine-acetylated histone binding(GO:0070577) |
| 1.4 | 26.6 | GO:0031492 | nucleosomal DNA binding(GO:0031492) |
| 0.9 | 25.6 | GO:0070888 | E-box binding(GO:0070888) |
| 0.3 | 25.2 | GO:0016881 | acid-amino acid ligase activity(GO:0016881) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.1 | 81.1 | PID MYC ACTIV PATHWAY | Validated targets of C-MYC transcriptional activation |
| 1.1 | 53.2 | PID AR PATHWAY | Coregulation of Androgen receptor activity |
| 1.0 | 51.4 | PID E2F PATHWAY | E2F transcription factor network |
| 1.1 | 48.4 | PID HNF3B PATHWAY | FOXA2 and FOXA3 transcription factor networks |
| 0.9 | 28.9 | PID P53 REGULATION PATHWAY | p53 pathway |
| 0.6 | 28.2 | PID NOTCH PATHWAY | Notch signaling pathway |
| 0.7 | 27.0 | PID REG GR PATHWAY | Glucocorticoid receptor regulatory network |
| 0.6 | 26.6 | PID P73PATHWAY | p73 transcription factor network |
| 0.9 | 26.1 | PID IGF1 PATHWAY | IGF1 pathway |
| 1.6 | 25.8 | PID SMAD2 3PATHWAY | Regulation of cytoplasmic and nuclear SMAD2/3 signaling |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.9 | 44.8 | REACTOME LOSS OF NLP FROM MITOTIC CENTROSOMES | Genes involved in Loss of Nlp from mitotic centrosomes |
| 0.8 | 43.9 | REACTOME MITOTIC PROMETAPHASE | Genes involved in Mitotic Prometaphase |
| 1.8 | 42.1 | REACTOME G0 AND EARLY G1 | Genes involved in G0 and Early G1 |
| 0.8 | 41.4 | REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM | Genes involved in Transport of Mature Transcript to Cytoplasm |
| 1.5 | 40.1 | REACTOME INTRINSIC PATHWAY FOR APOPTOSIS | Genes involved in Intrinsic Pathway for Apoptosis |
| 0.6 | 37.5 | REACTOME MRNA SPLICING | Genes involved in mRNA Splicing |
| 6.2 | 30.8 | REACTOME RNA POL I PROMOTER OPENING | Genes involved in RNA Polymerase I Promoter Opening |
| 1.2 | 27.7 | REACTOME NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING | Genes involved in Negative regulators of RIG-I/MDA5 signaling |
| 1.0 | 27.5 | REACTOME MEIOTIC SYNAPSIS | Genes involved in Meiotic Synapsis |
| 0.2 | 26.7 | REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION | Genes involved in Antigen processing: Ubiquitination & Proteasome degradation |