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 ADCY1

Basic gene info.	Gene symbol	ADCY1
	Gene name	adenylate cyclase 1 (brain)
	Synonyms	AC1\|DFNB44
	Cytomap	UCSC genome browser: 7p13-p12
	Genomic location	chr7 :45614124-45762714
	Type of gene	protein-coding
	RefGenes	NM_001281768.1, NM_021116.2,
	Ensembl id	ENSG00000164742
	Description	3',5'-cyclic AMP synthetaseATP pyrophosphate-lyase 1Ca(2+)/calmodulin-activated adenylyl cyclaseadenyl cyclaseadenylate cyclase type 1adenylate cyclase type Iadenylyl cyclase 1
	Modification date	20141207
dbXrefs	MIM : 103072
	HGNC : HGNC
	Ensembl : ENSG00000164742
	HPRD : 00053
	Vega : OTTHUMG00000155420
Protein	UniProt: Q08828 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ADCY1
	BioGPS: 107
	Gene Expression Atlas: ENSG00000164742
	The Human Protein Atlas: ENSG00000164742
Pathway	NCI Pathway Interaction Database: ADCY1
	KEGG: ADCY1
	REACTOME: ADCY1
	ConsensusPathDB
	Pathway Commons: ADCY1
Metabolism	MetaCyc: ADCY1
	HUMANCyc: ADCY1
Regulation	Ensembl's Regulation: ENSG00000164742
	miRBase: chr7 :45,614,124-45,762,714
	TargetScan: NM_001281768
	cisRED: ENSG00000164742
Context	iHOP: ADCY1
	cancer metabolism search in PubMed: ADCY1
	UCL Cancer Institute: ADCY1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ADCY1 in cancer cell metabolism	1. Li Y, Liang Q, Wen YQ, Chen LL, Wang LT, et al. (2010) Comparative proteomics analysis of human osteosarcomas and benign tumor of bone. Cancer Genet Cytogenet 198: 97-106. doi: 10.1016/j.cancergencyto.2010.01.003. go to article

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Phenotypic Information for ADCY1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ADCY1
	Familial Cancer Database: ADCY1

* 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	Therapeutic Vulnerabilities in Cancer¹

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,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_PURINE_METABOLISM REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM	103072; gene. 610154; phenotype.
Orphanet	90636; Autosomal recessive non-syndromic sensorineural deafness type DFNB.
Disease	KEGG Disease: ADCY1
	MedGen: ADCY1 (Human Medical Genetics with Condition)
	ClinVar: ADCY1
Phenotype	MGI: ADCY1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ADCY1

Mutations for ADCY1

* 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	ADCY1	chr7	45617247	45617267		chr7	567388	567408
ovary	ADCY1	chr7	45639825	45639845		chr7	45570899	45570919
ovary	ADCY1	chr7	45684854	45684874	ADCY1	chr7	45700086	45700106
ovary	ADCY1	chr7	45697837	45697857		chr7	51788473	51788493
ovary	ADCY1	chr7	45700648	45700668		chr7	51797055	51797075
skin	ADCY1	chr7	45662025	45662025	SLC30A4	chr15	45798748	45798748

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 ADCY1 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
BM693341	ADCY1	1	126	7	45754755	45754880	KDM3A	119	468	2	86719270	86719619
BM668617	KDM3A	24	587	2	86719270	86719833	ADCY1	580	654	7	45754806	45754880
BG315024	ADCY1	1	225	7	45761533	45761756	JUN	221	668	1	59248643	59249088
AU252813	ADCY1	1	225	7	45758694	45758918	ADCY1	223	654	7	45757167	45757593

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=7

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=156)	Stat. for Synonymous SNVs (# total SNVs=42)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted snv.

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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
chr7:45632382-45632382	p.V222I	4
chr7:45662327-45662327	p.F335F	4
chr7:45697426-45697426	p.D417N	4
chr7:45750217-45750217	p.R1008Q	4
chr7:45724608-45724608	p.R672C	3
chr7:45632476-45632476	p.R253Q	3
chr7:45750216-45750216	p.R1008W	3
chr7:45717651-45717651	p.R597W	3
chr7:45726166-45726166	p.R783H	3
chr7:45725619-45725619	p.S711L	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=6

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	2	4	1	28	4		12		4	1		22	11	4		1	27	20		18
# mutation	2	4	1	27	4		13		4	1		25	12	4		1	37	27		28
nonsynonymous SNV	1	3	1	20	4		12		3			17	10	4			22	15		21
synonymous SNV	1	1		7			1		1	1		8	2			1	15	12		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
chr7:45662327	p.F335F,ADCY1	3
chr7:45750216	p.R1008W	3
chr7:45750217	p.R1008Q	3
chr7:45717468	p.T401A,ADCY1	2
chr7:45725707	p.R412C,ADCY1	2
chr7:45717647	p.D417N,ADCY1	2
chr7:45697378	p.V595V	2
chr7:45632382	p.V222I	2
chr7:45697411	p.P740P	2
chr7:45697426	p.R536W	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 ADCY1 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 ADCY1

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


ADAM7,ADCY10,ALPI,ANKRD50,MPC2,DCAF6,DNAJC5B, DNAJC5G,ELFN2,FAM135B,FOXD4L2,G6PC2,GSTTP1,CFAP74, KLHL12,RAD21L1,TBX10,TEX19,TPCN2,TUBB7P,UNC5C	ABCC12,ACSM1,ADCY10,AKR1D1,C15orf43,CTNNA2,DDC, ELOVL7,EPS8L3,FMO5,HIST1H2AG,HIST1H3G,IDI1,IYD, LST-3TM12,RIMS1,SGPP2,SLC12A3,SLC26A6,TMPRSS11F,ZP2

ADCY10,ASUN,C12orf71,CASC1,DLK1,FGFR1OP2,GLIS3, GPR112,GRK1,KLHL42,KRAS,LOC100133893,LYRM5,MED21, MRPS35,NR5A1,PROL1,SLC23A3,STAR,STK38L,TM7SF3	ADAMTSL5,ADCY10,AGAP11,BCO2,C3orf35,DEFB131,ENAM, FTCD,GRIA4,HOXC11,HOXC6,HOXC8,KCNJ3,NLRP9, NODAL,NR1I3,SOX6,SPAM1,SUSD2,TBX3,TIAM2

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 ADCY1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q08828; -.
Chemistry	ChEMBL	CHEMBL2899; -.
Organism-specific databases	PharmGKB	PA24560; -.
Organism-specific databases	CTD	107; -.

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
DB00131	adenylate cyclase 1 (brain)	approved; nutraceutical	Adenosine monophosphate
DB00171	adenylate cyclase 1 (brain)	approved; nutraceutical	Adenosine triphosphate
DB00988	adenylate cyclase 1 (brain)	approved	Dopamine
DB00125	adenylate cyclase 1 (brain)	approved; nutraceutical	L-Arginine
DB00155	adenylate cyclase 1 (brain)	approved; nutraceutical	L-Citrulline
DB00435	adenylate cyclase 1 (brain)	approved	Nitric Oxide
DB00396	adenylate cyclase 1 (brain)	approved	Progesterone
DB00938	adenylate cyclase 1 (brain)	approved	Salmeterol

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Cross referenced IDs for ADCY1

* 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