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 ADCY1
Basic gene info.Gene symbolADCY1
Gene nameadenylate cyclase 1 (brain)
SynonymsAC1|DFNB44
CytomapUCSC genome browser: 7p13-p12
Genomic locationchr7 :45614124-45762714
Type of geneprotein-coding
RefGenesNM_001281768.1,
NM_021116.2,
Ensembl idENSG00000164742
Description3',5'-cyclic AMP synthetaseATP pyrophosphate-lyase 1Ca(2+)/calmodulin-activated adenylyl cyclaseadenyl cyclaseadenylate cyclase type 1adenylate cyclase type Iadenylyl cyclase 1
Modification date20141207
dbXrefs MIM : 103072
HGNC : HGNC
Ensembl : ENSG00000164742
HPRD : 00053
Vega : OTTHUMG00000155420
ProteinUniProt: Q08828
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ADCY1
BioGPS: 107
Gene Expression Atlas: ENSG00000164742
The Human Protein Atlas: ENSG00000164742
PathwayNCI Pathway Interaction Database: ADCY1
KEGG: ADCY1
REACTOME: ADCY1
ConsensusPathDB
Pathway Commons: ADCY1
MetabolismMetaCyc: ADCY1
HUMANCyc: ADCY1
RegulationEnsembl's Regulation: ENSG00000164742
miRBase: chr7 :45,614,124-45,762,714
TargetScan: NM_001281768
cisRED: ENSG00000164742
ContextiHOP: ADCY1
cancer metabolism search in PubMed: ADCY1
UCL Cancer Institute: ADCY1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ADCY1 in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM 103072; gene.
610154; phenotype.
Orphanet 90636; Autosomal recessive non-syndromic sensorineural deafness type DFNB.
DiseaseKEGG Disease: ADCY1
MedGen: ADCY1 (Human Medical Genetics with Condition)
ClinVar: ADCY1
PhenotypeMGI: ADCY1 (International Mouse Phenotyping Consortium)
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.

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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryADCY1chr74561724745617267chr7567388567408
ovaryADCY1chr74563982545639845chr74557089945570919
ovaryADCY1chr74568485445684874ADCY1chr74570008645700106
ovaryADCY1chr74569783745697857chr75178847351788493
ovaryADCY1chr74570064845700668chr75179705551797075
skinADCY1chr74566202545662025SLC30A4chr154579874845798748
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 ADCY1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM693341ADCY1112674575475545754880KDM3A11946828671927086719619
BM668617KDM3A2458728671927086719833ADCY158065474575480645754880
BG315024ADCY1122574576153345761756JUN22166815924864359249088
AU252813ADCY1122574575869445758918ADCY122365474575716745757593

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 1 1  1 1    1   
GAIN (# sample) 1 1    1    1   
LOSS (# sample)      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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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=7

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check002.gifSomatic 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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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
chr7:45632382-45632382p.V222I4
chr7:45662327-45662327p.F335F4
chr7:45697426-45697426p.D417N4
chr7:45750217-45750217p.R1008Q4
chr7:45632476-45632476p.R253Q3
chr7:45750216-45750216p.R1008W3
chr7:45717651-45717651p.R597W3
chr7:45726166-45726166p.R783H3
chr7:45725619-45725619p.S711L3
chr7:45662269-45662269p.A316V3

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample241284 12 41 22114 12720 18
# mutation241274 13 41 25124 13727 28
nonsynonymous SNV131204 12 3  17104  2215 21
synonymous SNV11 7  1 11 82  11512 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
chr7:45662327p.F335F,ADCY13
chr7:45750216p.R1008W3
chr7:45750217p.R1008Q3
chr7:45717468p.R412C,ADCY12
chr7:45725707p.D417N,ADCY12
chr7:45717647p.V222I2
chr7:45697378p.V595V2
chr7:45632382p.P740P2
chr7:45697411p.R536W2
chr7:45697426p.T401A,ADCY12

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 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

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

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
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 ADCY1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q08828; -.
ChemistryChEMBL CHEMBL2899; -.
Organism-specific databasesPharmGKB PA24560; -.
Organism-specific databasesCTD 107; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00131adenylate cyclase 1 (brain)approved; nutraceuticalAdenosine monophosphate
DB00171adenylate cyclase 1 (brain)approved; nutraceuticalAdenosine triphosphate
DB00988adenylate cyclase 1 (brain)approvedDopamine
DB00125adenylate cyclase 1 (brain)approved; nutraceuticalL-Arginine
DB00155adenylate cyclase 1 (brain)approved; nutraceuticalL-Citrulline
DB00435adenylate cyclase 1 (brain)approvedNitric Oxide
DB00396adenylate cyclase 1 (brain)approvedProgesterone
DB00938adenylate cyclase 1 (brain)approvedSalmeterol


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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



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