Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 ADCY5
Basic gene info.Gene symbolADCY5
Gene nameadenylate cyclase 5
SynonymsAC5|FDFM
CytomapUCSC genome browser: 3q21.1
Genomic locationchr3 :123001142-123135189
Type of geneprotein-coding
RefGenesNM_001199642.1,
NM_183357.2,
Ensembl idENSG00000173175
DescriptionATP pyrophosphate-lyase 5adenylate cyclase type 5adenylate cyclase type Vadenylyl cyclase 5
Modification date20141219
dbXrefs MIM : 600293
HGNC : HGNC
Ensembl : ENSG00000173175
HPRD : 08973
Vega : OTTHUMG00000159517
ProteinUniProt: O95622
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ADCY5
BioGPS: 111
Gene Expression Atlas: ENSG00000173175
The Human Protein Atlas: ENSG00000173175
PathwayNCI Pathway Interaction Database: ADCY5
KEGG: ADCY5
REACTOME: ADCY5
ConsensusPathDB
Pathway Commons: ADCY5
MetabolismMetaCyc: ADCY5
HUMANCyc: ADCY5
RegulationEnsembl's Regulation: ENSG00000173175
miRBase: chr3 :123,001,142-123,135,189
TargetScan: NM_001199642
cisRED: ENSG00000173175
ContextiHOP: ADCY5
cancer metabolism search in PubMed: ADCY5
UCL Cancer Institute: ADCY5
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for ADCY5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ADCY5
Familial Cancer Database: ADCY5
* 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/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM 600293; gene.
606703; phenotype.
Orphanet 324588; Familial dyskinesia and facial myokymia.
DiseaseKEGG Disease: ADCY5
MedGen: ADCY5 (Human Medical Genetics with Condition)
ClinVar: ADCY5
PhenotypeMGI: ADCY5 (International Mouse Phenotyping Consortium)
PhenomicDB: ADCY5

Mutations for ADCY5
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryADCY5chr3123095055123095075ADCY5chr3123098816123098836
ovaryADCY5chr3123119845123119865ADCY5chr3123121236123121256
ovaryADCY5chr3123129377123129397ADCY5chr3123129756123129776
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ADCY5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI037155ADCY511593123001294123001452GLIS115022715397955953979636
BI037157ADCY511593123001294123001452GLIS115022715397955953979636
DA952878ADCY514343123016332123016764ADCY54315553123018995123019119

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample  2       1      
GAIN (# sample)  2       1      
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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check002.gifSNV 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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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=134)
Stat. for Synonymous SNVs
(# total SNVs=45)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=3)

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr3:123005609-123005609p.P1194S3
chr3:123166520-123166520p.A291A3
chr3:123046525-123046525p.N629N3
chr3:123046533-123046533p.E627K3
chr3:123166285-123166285p.A370S3
chr3:123044280-123044280p.M659I3
chr3:123167249-123167249p.G48G3
chr3:123044289-123044289p.I656I3
chr3:123021952-123021952p.D892N2
chr3:123036942-123036942p.R760Q2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample562267 6 4122354  2213 17
# mutation562287 6 4122564  2817 21
nonsynonymous SNV151227 4 4111923  1713 14
synonymous SNV4116  2   1641  114 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr3:123005609p.S783S,ADCY53
chr3:123008730p.D609N,ADCY53
chr3:123018992p.N279N,ADCY53
chr3:123046525p.P844S,ADCY53
chr3:123010154p.E706K,ADCY52
chr3:123044275p.R410Q,ADCY52
chr3:123036942p.P695S,ADCY52
chr3:123051504p.R311H,ADCY52
chr3:123023025p.F466F,ADCY52
chr3:123005539p.R867L,ADCY52

check002.gifOther 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

check002.gifCopy Number for ADCY5 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 ADCY5

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

ACACB,ADCY5,ALMS1P,BAMBI,ELMSAN1,CNNM4,CNTD1,
CSF3R,DNMBP,FAM161B,HMGXB3,KANSL3,KMT2B___KMT2D,NUDT16,
PCDH1,PLAC4,RBM47,SLC4A8,TNRC6C,WNK4,ZNF423
ADCY5,AOC3,SYNE3,DOCK6,EHD2,FZD4,HEPN1,
HSPG2,KANK1,CTIF,LIPE,MCAM,MGLL,PTPRS,
RBPMS2,RDH5,SLC29A4,STXBP1,TLN1,TUSC5,TYRO3

ADCY5,AOC3,ASB2,BVES,CAND2,FHL1,GNAO1,
HSPB6,ITGA7,KIAA2022,LDB3,LMOD1,LONRF2,MAP6,
MYOCD,MYOM1,PDZRN4,PGR,SYNPO2,SYPL2,TNS1
ASIC1,ADCY5,AOC3,ATP2B4,CACNA1C,CACNA1H,COL15A1,
COL4A2,DCHS1,DYSF,FBXL7,ITGA7,ITIH5,LOC283174,
NPTXR,NRXN2,SETBP1,TEAD3,TLN1,TSPAN18,VCL
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 ADCY5
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB O95622; -.
ChemistryChEMBL CHEMBL2097167; -.
ChemistryGuidetoPHARMACOLOGY 1282; -.
Organism-specific databasesPharmGKB PA24563; -.
Organism-specific databasesCTD 111; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02587adenylate cyclase 5experimentalForskolin
DB06843adenylate cyclase 5experimental2',5'-DIDEOXY-ADENOSINE 3'-MONOPHOSPHATE
DB00938adenylate cyclase 5approvedSalmeterol


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Cross referenced IDs for ADCY5
* 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



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