Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	EP300
	Gene name	E1A binding protein p300
	Synonyms	KAT3B\|RSTS2\|p300
	Cytomap	UCSC genome browser: 22q13.2
	Genomic location	chr22 :41488613-41576081
	Type of gene	protein-coding
	RefGenes	NM_001429.3,
	Ensembl id	ENSG00000100393
	Description	E1A-associated protein p300E1A-binding protein, 300kDhistone acetyltransferase p300p300 HAT
	Modification date	20141222
dbXrefs	MIM : 602700
	HGNC : HGNC
	Ensembl : ENSG00000100393
	HPRD : 04078
	Vega : OTTHUMG00000150937
Protein	UniProt: Q09472 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EP300
	BioGPS: 2033
	Gene Expression Atlas: ENSG00000100393
	The Human Protein Atlas: ENSG00000100393
Pathway	NCI Pathway Interaction Database: EP300
	KEGG: EP300
	REACTOME: EP300
	ConsensusPathDB
	Pathway Commons: EP300
Metabolism	MetaCyc: EP300
	HUMANCyc: EP300
Regulation	Ensembl's Regulation: ENSG00000100393
	miRBase: chr22 :41,488,613-41,576,081
	TargetScan: NM_001429
	cisRED: ENSG00000100393
Context	iHOP: EP300
	cancer metabolism search in PubMed: EP300
	UCL Cancer Institute: EP300
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EP300 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	602700; gene. 613684; phenotype.
Orphanet	353284; Rubinstein-Taybi syndrome due to EP300 haploinsufficiency.
Disease	KEGG Disease: EP300
	MedGen: EP300 (Human Medical Genetics with Condition)
	ClinVar: EP300
Phenotype	MGI: EP300 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	EP300	chr22	41513022	41513042		chr22	47816718	47816738
ovary	EP300	chr22	41513329	41513349		chr8	144859393	144859413
ovary	EP300	chr22	41548603	41548623	EP300	chr22	41551591	41551611
ovary	EP300	chr22	41551203	41551223		chr22	41583055	41583075
ovary	EP300	chr22	41567335	41567355	XPNPEP3	chr22	41303626	41303646
ovary	EP300	chr22	41568672	41568692	EP300	chr22	41567248	41567268

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EP300 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AW366672	EP300	1	156	22	41573842	41573997	DAZAP2	152	229	12	51634135	51634212
AY187920	MLL	1	321	11	118353136	118355690	EP300	320	361	22	41547835	41547876
BE071569	LYRM1	22	99	16	20927209	20927287	EP300	88	226	22	41574542	41574680
DA384171	EP300	1	420	22	41521856	41523721	SPPL3	416	553	12	121211275	121211412
BE704331	LOC100505806	6	111	5	9550055	9550160	EP300	107	413	22	41544492	41544797
AL044228	TSPAN16	32	273	19	11435020	11435261	EP300	273	339	22	41573606	41573672
AW580958	EP300	1	54	22	41574952	41575005	EP300	54	273	22	41574978	41575197
BF915954	SPHK1	1	141	17	74383792	74383932	EP300	139	289	22	41574556	41574706
BF766544	RNF220	161	180	1	45109570	45109589	EP300	169	321	22	41545970	41546122

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr22:41565529-41565529	p.D1399Y	12
chr22:41572350-41572350	p.R1627W	8
chr22:41566475-41566475	p.H1451L	5
chr22:41566531-41566531	p.M1470fs*26	5
chr22:41564853-41564853	p.C1385Y	5
chr22:41569719-41569719	p.K1570N	4
chr22:41533773-41533773	p.R580Q	4
chr22:41572810-41572810	p.N1700fs*9	4
chr22:41572357-41572357	p.A1629V	4
chr22:41574377-41574377	p.P2221Q	3

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	15	5	1	58	5		19		8	3		4	9	1			16	17		17
# mutation	18	5	1	49	5		17		8	3		4	10	1			16	20		27
nonsynonymous SNV	16	4	1	35	3		16		6	2		1	8	1			12	16		22
synonymous SNV	2	1		14	2		1		2	1		3	2				4	4		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr22:41565529	p.D1399Y	7
chr22:41572350	p.R1627W	4
chr22:41548253	p.A1629V	3
chr22:41553402	p.E1013E	3
chr22:41569717	p.E1014G	3
chr22:41533773	p.R580Q	3
chr22:41569719	p.K1570E	3
chr22:41572266	p.K1570K	3
chr22:41572357	p.C1164Y	3
chr22:41548251	p.R1599S	3

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q09472; -.
Chemistry	ChEMBL	CHEMBL3784; -.
Chemistry	GuidetoPHARMACOLOGY	2735; -.
Organism-specific databases	PharmGKB	PA27807; -.
Organism-specific databases	CTD	2033; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00171	E1A binding protein p300	approved; nutraceutical	Adenosine triphosphate
DB00119	E1A binding protein p300	approved; nutraceutical	Pyruvic acid
DB01234	E1A binding protein p300	approved; investigational	Dexamethasone
DB00269	E1A binding protein p300	approved	Chlorotrianisene
DB00286	E1A binding protein p300	approved	Conjugated Estrogens
DB00890	E1A binding protein p300	approved	Dienestrol
DB00255	E1A binding protein p300	approved	Diethylstilbestrol
DB00783	E1A binding protein p300	approved; investigational	Estradiol
DB00655	E1A binding protein p300	approved	Estrone
DB00977	E1A binding protein p300	approved	Ethinyl 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