Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for EP300
Basic gene info.Gene symbolEP300
Gene nameE1A binding protein p300
SynonymsKAT3B|RSTS2|p300
CytomapUCSC genome browser: 22q13.2
Genomic locationchr22 :41488613-41576081
Type of geneprotein-coding
RefGenesNM_001429.3,
Ensembl idENSG00000100393
DescriptionE1A-associated protein p300E1A-binding protein, 300kDhistone acetyltransferase p300p300 HAT
Modification date20141222
dbXrefs MIM : 602700
HGNC : HGNC
Ensembl : ENSG00000100393
HPRD : 04078
Vega : OTTHUMG00000150937
ProteinUniProt: Q09472
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EP300
BioGPS: 2033
Gene Expression Atlas: ENSG00000100393
The Human Protein Atlas: ENSG00000100393
PathwayNCI Pathway Interaction Database: EP300
KEGG: EP300
REACTOME: EP300
ConsensusPathDB
Pathway Commons: EP300
MetabolismMetaCyc: EP300
HUMANCyc: EP300
RegulationEnsembl's Regulation: ENSG00000100393
miRBase: chr22 :41,488,613-41,576,081
TargetScan: NM_001429
cisRED: ENSG00000100393
ContextiHOP: EP300
cancer metabolism search in PubMed: EP300
UCL Cancer Institute: EP300
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EP300 in cancer cell metabolism1. Jeong E, Koo JE, Yeon SH, Kwak MK, Hwang DH, et al. (2014) PPARdelta deficiency disrupts hypoxia-mediated tumorigenic potential of colon cancer cells. Mol Carcinog 53: 926-937. doi: 10.1002/mc.22144. go to article
2. Yi P, Wang Z, Feng Q, Pintilie GD, Foulds CE, et al. (2015) Structure of a biologically active estrogen receptor-coactivator complex on DNA. Mol Cell 57: 1047-1058. doi: 10.1016/j.molcel.2015.01.025. pmid: 4369429. go to article
3. Sabari BR, Tang Z, Huang H, Yong-Gonzalez V, Molina H, et al. (2015) Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. Mol Cell 58: 203-215. doi: 10.1016/j.molcel.2015.02.029. go to article

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Phenotypic Information for EP300(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EP300
Familial Cancer Database: EP300
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in BLCA 6, HNSC 7, UCEC 8,

Therapeutic Vulnerabilities in Cancer9

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
6 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12965.html,
7 https://www.sciencemag.org/content/333/6046/1157,
8 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
9Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 602700; gene.
613684; phenotype.
Orphanet 353284; Rubinstein-Taybi syndrome due to EP300 haploinsufficiency.
DiseaseKEGG Disease: EP300
MedGen: EP300 (Human Medical Genetics with Condition)
ClinVar: EP300
PhenotypeMGI: EP300 (International Mouse Phenotyping Consortium)
PhenomicDB: EP300

Mutations for EP300
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryEP300chr224151302241513042chr224781671847816738
ovaryEP300chr224151332941513349chr8144859393144859413
ovaryEP300chr224154860341548623EP300chr224155159141551611
ovaryEP300chr224155120341551223chr224158305541583075
ovaryEP300chr224156733541567355XPNPEP3chr224130362641303646
ovaryEP300chr224156867241568692EP300chr224156724841567268
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EP300 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW366672EP3001156224157384241573997DAZAP2152229125163413551634212
AY187920MLL132111118353136118355690EP300320361224154783541547876
BE071569LYRM12299162092720920927287EP30088226224157454241574680
DA384171EP3001420224152185641523721SPPL341655312121211275121211412
BE704331LOC1005058066111595500559550160EP300107413224154449241544797
AL044228TSPAN1632273191143502011435261EP300273339224157360641573672
AW580958EP300154224157495241575005EP30054273224157497841575197
BF915954SPHK11141177438379274383932EP300139289224157455641574706
BF766544RNF22016118014510957045109589EP300169321224154597041546122

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1  1    1 2  1   
GAIN (# sample)1       1    1   
LOSS (# sample)   1      2      
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=12

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=238)
Stat. for Synonymous SNVs
(# total SNVs=50)
Stat. for Deletions
(# total SNVs=23)
Stat. for Insertions
(# total SNVs=10)

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr22:41565529-41565529p.D1399Y12
chr22:41572350-41572350p.R1627W8
chr22:41566475-41566475p.H1451L5
chr22:41566531-41566531p.M1470fs*265
chr22:41564853-41564853p.C1385Y5
chr22:41533773-41533773p.R580Q4
chr22:41572357-41572357p.A1629V4
chr22:41569719-41569719p.K1570N4
chr22:41572810-41572810p.N1700fs*94
chr22:41572903-41572903p.S1730fs*43

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=8

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1551585 19 83 491  1617 17
# mutation1851495 17 83 4101  1620 27
nonsynonymous SNV1641353 16 62 181  1216 22
synonymous SNV21 142 1 21 32   44 5
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr22:41565529p.D1399Y7
chr22:41572350p.R1627W4
chr22:41548251p.A1629V3
chr22:41548253p.E1013E3
chr22:41553402p.E1014G3
chr22:41569717p.R580Q3
chr22:41533773p.K1570E3
chr22:41569719p.K1570K3
chr22:41572266p.C1164Y3
chr22:41572357p.R1599S3

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for EP300 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for EP300

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

ASXL2,BIRC6,PRR14L,CCNT1,DPP8,EP300,EXOC6B,
FAM63B,GTF2A1,LATS1,LDOC1L,MTMR3,PEX26,RAD54L2,
REST,SON,TNRC6B,TTBK2,UHMK1,WDFY3,ZNF81
ASH1L,BIRC6,BOD1L1,BPTF,C11orf30,CCNT1,EP300,
GTF2A1,EPG5,LATS1,LMTK2,KMT2C,KMT2A,MYO9A,
KAT6A,NCOA2,REST,RSF1,SBNO1,SPEN,ZKSCAN8

ASXL2,PRR14L,SPECC1L,EP300,FAM168A,GTF2A1,HERC1,
LATS1,LDOC1L,MED13L,KMT2B___KMT2D,MYO9A,NCOA2,PI4KA,
REST,SOS1,SPEN,TAOK1,TTBK2,ZNF106,ZNF609
ARID1A,ATXN1L,BOD1L1,BPTF,HECTD4,CHD8,CREBBP,
DIDO1,EP300,EP400,GON4L,KDM2A,MED12,MED13L,
KMT2C,KAT6A,SON,SPEN,SRCAP,TRRAP,VPS13D
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for EP300
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q09472; -.
ChemistryChEMBL CHEMBL3784; -.
ChemistryGuidetoPHARMACOLOGY 2735; -.
Organism-specific databasesPharmGKB PA27807; -.
Organism-specific databasesCTD 2033; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00171E1A binding protein p300approved; nutraceuticalAdenosine triphosphate
DB00119E1A binding protein p300approved; nutraceuticalPyruvic acid
DB01234E1A binding protein p300approved; investigationalDexamethasone
DB00269E1A binding protein p300approvedChlorotrianisene
DB00286E1A binding protein p300approvedConjugated Estrogens
DB00890E1A binding protein p300approvedDienestrol
DB00255E1A binding protein p300approvedDiethylstilbestrol
DB00783E1A binding protein p300approved; investigationalEstradiol
DB00655E1A binding protein p300approvedEstrone
DB00977E1A binding protein p300approvedEthinyl Estradiol


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Cross referenced IDs for EP300
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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