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 ADCY8

Basic gene info.	Gene symbol	ADCY8
	Gene name	adenylate cyclase 8 (brain)
	Synonyms	AC8\|ADCY3\|HBAC1
	Cytomap	UCSC genome browser: 8q24
	Genomic location	chr8 :131792546-132052835
	Type of gene	protein-coding
	RefGenes	NM_001115.2,
	Ensembl id	ENSG00000155897
	Description	ATP pyrophosphate-lyase 8adenylate cyclase type 8adenylate cyclase type VIIIadenylyl cyclase 8adenylyl cyclase-8, brainca(2+)/calmodulin-activated adenylyl cyclase
	Modification date	20141222
dbXrefs	MIM : 103070
	HGNC : HGNC
	Ensembl : ENSG00000155897
	HPRD : 00051
	Vega : OTTHUMG00000164756
Protein	UniProt: P40145 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ADCY8
	BioGPS: 114
	Gene Expression Atlas: ENSG00000155897
	The Human Protein Atlas: ENSG00000155897
Pathway	NCI Pathway Interaction Database: ADCY8
	KEGG: ADCY8
	REACTOME: ADCY8
	ConsensusPathDB
	Pathway Commons: ADCY8
Metabolism	MetaCyc: ADCY8
	HUMANCyc: ADCY8
Regulation	Ensembl's Regulation: ENSG00000155897
	miRBase: chr8 :131,792,546-132,052,835
	TargetScan: NM_001115
	cisRED: ENSG00000155897
Context	iHOP: ADCY8
	cancer metabolism search in PubMed: ADCY8
	UCL Cancer Institute: ADCY8
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ADCY8 in cancer cell metabolism	1. Liu Y, Chen SH, Li YM (2012) [Differential expression profiles of genes and miRNAs in alcoholic hepatitis]. Zhonghua Gan Zang Bing Za Zhi 20: 883-887. doi: 10.3760/cma.j.issn.1007-3418.2012.12.002. go to article

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Phenotypic Information for ADCY8(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ADCY8
	Familial Cancer Database: ADCY8

* 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	103070; gene.
Orphanet
Disease	KEGG Disease: ADCY8
	MedGen: ADCY8 (Human Medical Genetics with Condition)
	ClinVar: ADCY8
Phenotype	MGI: ADCY8 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ADCY8

Mutations for ADCY8

* 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	ADCY8	chr8	131975433	131975433		chr18	20269453	20269453
ovary	ADCY8	chr8	131897415	131897435	ADCY8	chr8	131857945	131857965
ovary	ADCY8	chr8	131908526	131908546	ADCY8	chr8	131916076	131916096
ovary	ADCY8	chr8	131997335	131997355	ADCY8	chr8	131975330	131975350
ovary	ADCY8	chr8	132000898	132000918		chr12	28253677	28253697
ovary	ADCY8	chr8	132033952	132033972	SNTB1	chr8	121735369	121735389
ovary	ADCY8	chr8	132037608	132037628	ADCY8	chr8	132042576	132042596
ovary	ADCY8	chr8	132046649	132046669		chr11	26776972	26776992
pancreas	ADCY8	chr8	131953488	131953508		chr8	130504278	130504298
pancreas	ADCY8	chr8	131987992	131988012	ADCY8	chr8	131988353	131988373
prostate	ADCY8	chr8	131964303	131964303		chr11	98350729	98350729

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 ADCY8 related fusion information.

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

BQ345242

ADCY8

478

131890511

131890902

DNAJC14

470

632

56216172

56216430

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	6	2		2			7		4		4				1		1
GAIN (# sample)	6	1		2			7		4		4				1		1
LOSS (# sample)	1	1

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=220)	Stat. for Synonymous SNVs (# total SNVs=81)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=0)
	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
chr8:131826458-131826458	p.R924C	6
chr8:131792904-131792904	p.G1163E	6
chr8:131916177-131916177	p.T584T	5
chr8:131848567-131848567	p.Y877Y	4
chr8:131812757-131812757	p.A992E	3
chr8:131880139-131880139	p.I721I	3
chr8:132052131-132052131	p.R150Q	3
chr8:131861945-131861945	p.R772Q	3
chr8:131916126-131916126	p.I601I	3
chr8:131921973-131921973	p.E541K	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=4

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	6	12	1	34	2		14	1	8	2		39	20	2	1	3	65	30	2	21
# mutation	6	12	1	43	2		15	1	9	2		47	24	2	1	3	79	32	2	27
nonsynonymous SNV	6	8		30	2		12	1	9	1		31	18	2	1	2	45	21	1	22
synonymous SNV		4	1	13			3			1		16	6			1	35	11	1	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
chr8:131916126	p.I601I	4
chr8:132002665	p.I582I	3
chr8:131880139	p.G547G	3
chr8:131916177	p.G1163E	3
chr8:131916288	p.R362S	3
chr8:131792904	p.R924C	3
chr8:131916183	p.I721I	3
chr8:131826458	p.T584T	3
chr8:131916094	p.R772W	2
chr8:131922053	p.G1102G	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 ADCY8 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 ADCY8

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


ADCY8,CHST1,CTTNBP2,DDX25,DKK4,EIF4E1B,FCRLB, FZD10,HTR1E,INSM1,KIAA0087,LRP2,MLN,OR8S1, OTX2,P2RX6P,PDZK1P1,SCUBE1,SLC35D3,SNAR-E,TUBA3E	ADCY8,C1orf68,C2,CCL13,CCR1,CD163,CD33, DNM1,ECM1,EMP3,GAP43,GPNMB,KIRREL3,MARCO, NXF3,SLC7A7,SPOCK1,SSC5D,TMEM106A,VCAN,VSIG4

AADAC,ADCY8,BAALC,CCR4,CLC,CSN2,FAM138D, GABRR3,IL36B,LOC116437,LOC283856,LOC728392,LRRC7,OR4D1, OR6B1,PNLIPRP3,RXRG,SPATA22,TFPI2,VWA5B1,VWC2L	ADCY8,ETNPPL,AHNAK,CDY2B,CSRP3,FAM131B,FAM19A4, LOC151658,LRRFIP1,MYOCD,OPN5,OR2F1,PIP5K1C,POU4F2, PTCHD1,PZP,RIMS3,RXFP2,SNX19,TMEM189,ZYG11B

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 ADCY8

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2097167; -.
Organism-specific databases	PharmGKB	PA29; -.
Organism-specific databases	CTD	114; -.

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
DB01033	adenylate cyclase 8 (brain)	approved	Mercaptopurine
DB00563	adenylate cyclase 8 (brain)	approved	Methotrexate
DB00938	adenylate cyclase 8 (brain)	approved	Salmeterol

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Cross referenced IDs for ADCY8

* 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