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 ADCY9

Basic gene info.	Gene symbol	ADCY9
	Gene name	adenylate cyclase 9
	Synonyms	AC9
	Cytomap	UCSC genome browser: 16p13.3
	Genomic location	chr16 :4012649-4166186
	Type of gene	protein-coding
	RefGenes	NM_001116.3,
	Ensembl id	ENSG00000162104
	Description	ATP pyrophosphate-lyase 9adenylate cyclase type 9adenylate cyclase type IXadenylyl cyclase 9type IX ATP pyrophosphate-lyase
	Modification date	20141207
dbXrefs	MIM : 603302
	HGNC : HGNC
	Ensembl : ENSG00000162104
	HPRD : 04489
	Vega : OTTHUMG00000177612
Protein	UniProt: O60503 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ADCY9
	BioGPS: 115
	Gene Expression Atlas: ENSG00000162104
	The Human Protein Atlas: ENSG00000162104
Pathway	NCI Pathway Interaction Database: ADCY9
	KEGG: ADCY9
	REACTOME: ADCY9
	ConsensusPathDB
	Pathway Commons: ADCY9
Metabolism	MetaCyc: ADCY9
	HUMANCyc: ADCY9
Regulation	Ensembl's Regulation: ENSG00000162104
	miRBase: chr16 :4,012,649-4,166,186
	TargetScan: NM_001116
	cisRED: ENSG00000162104
Context	iHOP: ADCY9
	cancer metabolism search in PubMed: ADCY9
	UCL Cancer Institute: ADCY9
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for ADCY9(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ADCY9
	Familial Cancer Database: ADCY9

* 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	603302; gene. 603302; gene.
Orphanet
Disease	KEGG Disease: ADCY9
	MedGen: ADCY9 (Human Medical Genetics with Condition)
	ClinVar: ADCY9
Phenotype	MGI: ADCY9 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ADCY9

Mutations for ADCY9

* 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	ADCY9	chr16	4082502	4082522	ADCY9	chr16	4098016	4098036
ovary	ADCY9	chr16	4114926	4114946	ADCY9	chr16	4117140	4117160
pancreas	ADCY9	chr16	4144271	4144291		chr16	4166921	4166941
pancreas	ADCY9	chr16	4157492	4157512	ADCY9	chr16	4102076	4102096

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 ADCY9 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
BF871520	ADCY9	1	68	16	4099044	4099111	BGN	59	160	X	152774633	152774735
BF854283	ADCY9	9	173	16	4159374	4159539	CTDSPL	171	455	3	38025332	38025616

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=119)	Stat. for Synonymous SNVs (# total SNVs=50)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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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
chr16:4042225-4042225	p.S710L	3
chr16:4016009-4016009	p.E1277K	3
chr16:4165432-4165432	p.P4P	3
chr16:4029168-4029168	p.P876P	3
chr16:4165068-4165068	p.A126T	2
chr16:4015810-4015810	p.E1343G	2
chr16:4016604-4016604	p.G1078G	2
chr16:4042224-4042224	p.S710S	2
chr16:4016249-4016249	p.M1197V	2
chr16:4015811-4015811	p.E1343K	2

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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	3	9	3	25	5		4	1	3	2		9	3	9	1	2	15	16	3	16
# mutation	3	9	3	23	5		5	1	4	2		9	3	9	1	2	16	19	3	28
nonsynonymous SNV	3	8	2	15	4		4		3	1		6	3	5		1	9	8	3	22
synonymous SNV		1	1	8	1		1	1	1	1		3		4	1	1	7	11		6

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
chr16:4029168	p.P876P	4
chr16:4163814	p.E544K	3
chr16:4042225	p.S710L	3
chr16:4016169	p.A126T	2
chr16:4042224	p.E391K	2
chr16:4043500	p.F1223F	2
chr16:4015908	p.S632S	2
chr16:4027524	p.A929A	2
chr16:4016249	p.M1197V	2
chr16:4165068	p.S710S	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 ADCY9 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 ADCY9

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


ABAT,ADCY9,APBB2,CA12,COG7,COQ7,CREBBP, EPB41L5,GLYR1,C5AR2,KIAA0556,MARVELD2,MKL2,PDPK1, JADE2,RAB11FIP3,SRRM2,ZNF174,ZSCAN32,ZNF552,ZNF91	ACTC1,ADCY9,AKAP6,BVES,C20orf166-AS1,CAND2,CEP85, FLNC,GATS,HSPA2,JPH2,LOC389333,MEF2D,MUSTN1, NEXN,PLN,PRKG1,SGCA,SPEG,SVIL,TPM2

ADCY9,AHDC1,AHNAK,AKAP13,CIC,CREBBP,CRYBG3, FRY,GBF1,HSPG2,IL6ST,KIAA0226,KIAA0247,LHFPL2, NDST1,NFIC,RAPGEF1,PEAK1,SKI,TLN1,ZMIZ1	ADCY9,AGPAT3,ARHGEF11,ATG9A,ATP6V0A1,BAG6,CDC42BPB, DENND1A,AGO1,FAT1,ARHGAP35,LAMP1,LRP5,NFE2L1, OGDH,RNF123,SEMA6A,SORT1,TGOLN2,TRAK1,UBR4

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 ADCY9

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2097167; -.
Chemistry	ChEMBL	CHEMBL2097167; -.
Organism-specific databases	PharmGKB	PA30; -.
Organism-specific databases	PharmGKB	PA30; -.
Organism-specific databases	CTD	115; -.
Organism-specific databases	CTD	115; -.

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
DB01064	adenylate cyclase 9	approved	Isoproterenol
DB00938	adenylate cyclase 9	approved	Salmeterol

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Cross referenced IDs for ADCY9

* 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