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 CREBBP

Basic gene info.	Gene symbol	CREBBP
	Gene name	CREB binding protein
	Synonyms	CBP\|KAT3A\|RSTS
	Cytomap	UCSC genome browser: 16p13.3
	Genomic location	chr16 :3775055-3930121
	Type of gene	protein-coding
	RefGenes	NM_001079846.1, NM_004380.2,
	Ensembl id	ENSG00000005339
	Description	CREB-binding protein
	Modification date	20141219
dbXrefs	MIM : 600140
	HGNC : HGNC
	Ensembl : ENSG00000005339
	HPRD : 02534
	Vega : OTTHUMG00000129431
Protein	UniProt: Q92793 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CREBBP
	BioGPS: 1387
	Gene Expression Atlas: ENSG00000005339
	The Human Protein Atlas: ENSG00000005339
Pathway	NCI Pathway Interaction Database: CREBBP
	KEGG: CREBBP
	REACTOME: CREBBP
	ConsensusPathDB
	Pathway Commons: CREBBP
Metabolism	MetaCyc: CREBBP
	HUMANCyc: CREBBP
Regulation	Ensembl's Regulation: ENSG00000005339
	miRBase: chr16 :3,775,055-3,930,121
	TargetScan: NM_001079846
	cisRED: ENSG00000005339
Context	iHOP: CREBBP
	cancer metabolism search in PubMed: CREBBP
	UCL Cancer Institute: CREBBP
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CREBBP in cancer cell metabolism	1. Lastowska M, Al-Afghani H, Al-Balool HH, Sheth H, Mercer E, et al. (2013) Identification of a neuronal transcription factor network involved in medulloblastoma development. Acta Neuropathol Commun 1: 35. doi: 10.1186/2051-5960-1-35. pmid: 3893591. go to article 2. Loeffler M, Kreuz M, Haake A, Hasenclever D, Trautmann H, et al. (2015) Genomic and epigenomic co-evolution in follicular lymphomas. Leukemia 29: 456-463. doi: 10.1038/leu.2014.209. go to article 3. Song Y, Li L, Ou Y, Gao Z, Li E, et al. (2014) Identification of genomic alterations in oesophageal squamous cell cancer. Nature 509: 91-95. doi: 10.1038/nature13176. go to article 4. Green MR, Kihira S, Liu CL, Nair RV, Salari R, et al. (2015) Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proc Natl Acad Sci U S A 112: E1116-1125. doi: 10.1073/pnas.1501199112. pmid: 4364211 go to article

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

Cancer Description
Cancer	CGAP: CREBBP
	Familial Cancer Database: CREBBP

* 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, DLBCL ⁷,	Therapeutic Vulnerabilities in Cancer⁸

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 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
8Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	180849; phenotype. 600140; gene.
Orphanet	353277; Rubinstein-Taybi syndrome due to CREBBP mutations. 353281; Rubinstein-Taybi syndrome due to 16p13.3 microdeletion. 370026; Acute myeloid leukemia with t(8;16)(p11;p13) translocation.
Disease	KEGG Disease: CREBBP
	MedGen: CREBBP (Human Medical Genetics with Condition)
	ClinVar: CREBBP
Phenotype	MGI: CREBBP (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CREBBP

Mutations for CREBBP

* 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
breast	CREBBP	chr16	3891365	3891365	CREBBP	chr16	3924308	3924308
central_nervous_system	CREBBP	chr16	3879875	3879875	CREBBP	chr16	3784982	3784982
ovary	CREBBP	chr16	3782438	3782458	CREBBP	chr16	3859503	3859523
ovary	CREBBP	chr16	3789179	3789199	CREBBP	chr16	3789808	3789828
ovary	CREBBP	chr16	3794208	3794228	SPRED3	chr19	38884658	38884678
ovary	CREBBP	chr16	3812960	3812980	CREBBP	chr16	3799320	3799340
ovary	CREBBP	chr16	3860777	3860797		chr19	54280926	54280946
ovary	CREBBP	chr16	3860787	3860807	CREBBP	chr16	3861465	3861485
ovary	CREBBP	chr16	3861129	3861149	CREBBP	chr16	3861198	3861218
ovary	CREBBP	chr16	3861466	3861486	CREBBP	chr16	3860302	3860322
pancreas	CREBBP	chr16	3801955	3801975	HS3ST2	chr16	22866560	22866580
pancreas	CREBBP	chr16	3846431	3846451	HS3ST2	chr16	22866797	22866817
pancreas	CREBBP	chr16	3914877	3914897	CREBBP	chr16	3916804	3916824

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 CREBBP 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
AA828778	CREBBP	1	157	16	3807883	3808040	CREBBP	155	220	16	3807820	3807885
BI000845	CREBBP	1	219	16	3781792	3786109	CREB3L2	210	296	7	137584036	137584122
AJ299262	CREBBP	1	110	16	3929833	3929942	KAT6B	109	308	10	76788245	76788444
AJ251845	CREBBP	1	110	16	3929833	3929942	KAT6A	109	229	8	41792267	41792387
AJ251843	KAT6A	1	188	8	41794774	41794961	CREBBP	188	1128	16	3843578	3901011
AJ251844	KAT6A	1	188	8	41794774	41794961	CREBBP	188	415	16	3843578	3860781
DA778521	EIF4E2	1	110	2	233415394	233421174	CREBBP	107	561	16	3830756	3832912
AJ299261	KAT6B	1	261	10	76784747	76785007	CREBBP	262	426	16	3900846	3901010
BG992160	SIAH1	284	331	16	48454762	48454810	CREBBP	328	609	16	3797210	3797493
BE156640	CREBBP	8	219	16	3831238	3832825	CREBBP	214	360	16	3820923	3823833
H19810	GGT7	1	182	20	33433152	33437803	CREBBP	183	441	16	3776978	3777235
BI033650	SNAP25	2	178	20	10287792	10287974	CREBBP	167	398	16	3784039	3784271
AJ315152	KAT6A	1	260	8	41793259	41793518	CREBBP	259	480	16	3926965	3927186
AY442917	KAT6A	1	54	8	41793795	41793848	CREBBP	55	110	16	3907401	3907456
AJ315158	KAT6A	1	277	8	41793759	41794035	CREBBP	272	480	16	3925853	3926060
BI003567	CREBBP	62	200	16	3843489	3843628	CREBBP	195	302	16	3860608	3860715
AJ315157	CREBBP	1	290	16	3926071	3926360	KAT6A	291	419	8	41793629	41793757
AJ315154	KAT6A	1	340	8	41792414	41792753	CREBBP	339	428	16	3926725	3926814
AK094404	CREBBP	1	1291	16	3918046	3919337	CREBBP	1279	2176	16	3916861	3917758
AY442918	CREBBP	1	58	16	3907347	3907404	KAT6A	58	105	8	41793857	41793904
AJ315151	CREBBP	1	211	16	3927349	3927559	KAT6A	211	464	8	41793018	41793271
BI049383	CARKD	6	241	13	111291696	111291930	CREBBP	236	404	16	3830869	3832739
BE701823	CREBBP	24	98	16	3776992	3777067	CREBBP	95	226	16	3777048	3777179
U89354	CREBBP	1	744	16	3777548	3778291	TNR	727	746	1	175441100	175441119

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=32

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=414)	Stat. for Synonymous SNVs (# total SNVs=73)

Stat. for Deletions (# total SNVs=30)	Stat. for Insertions (# total SNVs=12)

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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
chr16:3788618-3788618	p.R1446G	20
chr16:3788617-3788617	p.R1446H	12
chr16:3807902-3807902	p.R1173*	7
chr16:3786705-3786705	p.W1502C	7
chr16:3781328-3781330	p.S1680delS	6
chr16:3820773-3820773	p.S893L	6
chr16:3786704-3786704	p.Y1503H	6
chr16:3790512-3790512	p.R1341*	5
chr16:3786078-3786078	p.R1563G	5
chr16:3786703-3786703	p.Y1503F	5

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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=5

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	14	7	5	76	5		18		5	2		16	18	7	1	2	24	31		26
# mutation	13	7	5	78	4		18		5	2		19	20	7	1	2	27	38		36
nonsynonymous SNV	11	6	4	52	3		12		4	2		17	15	6	1		18	27		29
synonymous SNV	2	1	1	26	1		6		1			2	5	1		2	9	11		7

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
chr16:3786078	p.R1525G,CREBBP	5
chr16:3788618	p.R1408C,CREBBP	4
chr16:3778767	p.P2056L,CREBBP	3
chr16:3788651	p.D1397H,CREBBP	3
chr16:3843433	p.K1282K,CREBBP	2
chr16:3786763	p.R1131C,CREBBP	2
chr16:3900321	p.Q1041R,CREBBP	2
chr16:3778624	p.L2104M,CREBBP	2
chr16:3900364	p.P722S,CREBBP	2
chr16:3801786	p.A259T,CREBBP	2

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 CREBBP 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 CREBBP

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


SLX4,CRAMP1L,CREBBP,ERCC4,GLYR1,KDM3B,KIAA0430, KIAA0556,LOC100190986,LOC100271836,LOC652276,MKL2,PDPK1,SNX29, SMG1,SRCAP,SRRM2,THUMPD1,TNRC6A,UBN1,ZSCAN32	ARID1B,BRPF3,CHD2,CHD6,CREBBP,EP300,EP400, GPATCH8,KDM3B,LMTK2,MDN1,MED12,KMT2A,NCOA2, RAPGEF6,SMCR8,SPEN,SRRM2,TRRAP,ZNF142,ZNF827

ARID1B,ATXN1L,CRAMP1L,CREBBP,CTDSP2,EP300,FAM168A, GLTSCR1L,KIAA0430,KIDINS220,MED13L,MKL2,KMT2B___KMT2D,KMT2C, KMT2A,NFATC3,PDPK1,SMG1,SPEN,UBN1,ZNF500	ATXN1L,PRRC2B,HECTD4,CHD8,CREBBP,DIDO1,DYNC1H1, EP300,EP400,FAM193A,GIGYF2,HERC2,HUWE1,MED12, MED13L,KAT6A,KAT6B,NCOR2,SMARCA2,SMG6,SNRNP200

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 CREBBP

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q92793; -.
Chemistry	ChEMBL	CHEMBL5747; -.
Chemistry	GuidetoPHARMACOLOGY	2734; -.
Organism-specific databases	PharmGKB	PA26866; -.
Organism-specific databases	CTD	1387; -.

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
DB00619	CREB binding protein	approved	Imatinib
DB01234	CREB binding protein	approved; investigational	Dexamethasone
DB00864	CREB binding protein	approved; investigational	Tacrolimus
DB00171	CREB binding protein	approved; nutraceutical	Adenosine triphosphate
DB00269	CREB binding protein	approved	Chlorotrianisene
DB00286	CREB binding protein	approved	Conjugated Estrogens
DB00890	CREB binding protein	approved	Dienestrol
DB00255	CREB binding protein	approved	Diethylstilbestrol
DB00783	CREB binding protein	approved; investigational	Estradiol
DB00655	CREB binding protein	approved	Estrone
DB00977	CREB binding protein	approved	Ethinyl Estradiol

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Cross referenced IDs for CREBBP

* 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