Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 ADI1
Basic gene info.Gene symbolADI1
Gene nameacireductone dioxygenase 1
SynonymsAPL1|ARD|Fe-ARD|MTCBP1|Ni-ARD|SIPL|mtnD
CytomapUCSC genome browser: 2p25.3
Genomic locationchr2 :3501689-3523350
Type of geneprotein-coding
RefGenesNM_018269.3,
Ensembl idENSG00000182551
Description1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenaseARDMT1-MMP cytoplasmic tail-binding protein-1MTCBP-1acireductone dioxygenase (Fe(2+)-requiring)acireductone dioxygenase (Ni(2+)-requiring)fe-ARDmembrane-type 1 matrix metalloproteinase cytoplasmic
Modification date20141207
dbXrefs MIM : 613400
HGNC : HGNC
Ensembl : ENSG00000182551
HPRD : 17607
Vega : OTTHUMG00000112441
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ADI1
BioGPS: 55256
Gene Expression Atlas: ENSG00000182551
The Human Protein Atlas: ENSG00000182551
PathwayNCI Pathway Interaction Database: ADI1
KEGG: ADI1
REACTOME: ADI1
ConsensusPathDB
Pathway Commons: ADI1
MetabolismMetaCyc: ADI1
HUMANCyc: ADI1
RegulationEnsembl's Regulation: ENSG00000182551
miRBase: chr2 :3,501,689-3,523,350
TargetScan: NM_018269
cisRED: ENSG00000182551
ContextiHOP: ADI1
cancer metabolism search in PubMed: ADI1
UCL Cancer Institute: ADI1
Assigned class in ccmGDBC

Top
Phenotypic Information for ADI1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ADI1
Familial Cancer Database: ADI1
* 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_CYSTEINE_AND_METHIONINE_METABOLISM
REACTOME_SULFUR_AMINO_ACID_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES
REACTOME_METABOLISM_OF_POLYAMINES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ADI1
MedGen: ADI1 (Human Medical Genetics with Condition)
ClinVar: ADI1
PhenotypeMGI: ADI1 (International Mouse Phenotyping Consortium)
PhenomicDB: ADI1

Mutations for ADI1
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasADI1chr235215823521602chr8128759951128759971
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 ADI1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM353985ADI11272235023953502455ADI170181235023033502414
AA351447ZNF626190192084425020844339ADI190406235046253518634
BF095880ADI11432235025013504659TUBB6429487181232607612326134
CK904967ADI11189235022263502414ADI1187247235023953502455
CV569358ADI144478235023503502784ADI1472588235022243502339
BM456873ADI1277235232043523279TRIM14708779100848713100849516

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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample 1               
GAIN (# sample) 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)

Top
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=3

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=6)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr2:3502845-3502845p.T143T3
chr2:3504687-3504687p.D106D3
chr2:3502844-3502844p.K144E2
chr2:3517712-3517712p.L52L2
chr2:3504690-3504690p.F105F1
chr2:3517692-3517692p.R59K1
chr2:3502849-3502849p.Y142C1
chr2:3504598-3504598p.T136M1
chr2:3517727-3517727p.E47E1
chr2:3504605-3504605p.R134C1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   3  1 1  3 1  31 1
# mutation   3  1 1  3 1  31 1
nonsynonymous SNV   2    1  1 1  21  
synonymous SNV   1  1    2    1  1
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])

Top
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
chr2:3502844p.K144E2
chr2:3504690p.F105F2
chr2:3517727p.R168L1
chr2:3502845p.T143T1
chr2:3502849p.Y142C1
chr2:3504598p.T136M1
chr2:3504605p.R134C1
chr2:3504621p.P128P1
chr2:3504654p.I117I1
chr2:3504658p.R116Q1

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 ADI1 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]

Top
Gene Expression for ADI1

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ACP1,ADI1,C12orf45,PTRHD1,COMMD1,COX4I1,CPSF3,
DGUOK,DTNB,FAM58A,MFSD2B,NOL10,PDIA6,RNASEH1,
RPS7,SF3B14,SNRPG,TSSC1,TRAPPC12,UQCRH,UQCRHL
ACOT13,ACTR1A,ADI1,ATP5G3,ATP5H,ATP5J,ATP6V1E1,
C22orf39,PRADC1,CYSTM1,CHCHD4,EIF2B3,GTF3A,LDHA,
MGST3,MSRB2,NDUFA6,PSMC1,RILP,SLC25A20,SNAPIN

ACP1,ADI1,COX14,PTRHD1,CISD2,CNIH1,COMMD1,
COX6A1,COX7A2L,DUSP11,MDH1,MRPL44,MRPL54,MYEOV2,
NDUFS3,NOP10,ORC4,OST4,POLE4,PPA2,SUCLG1
ADI1,BDH2,LINC00324,TMEM256,SMIM20,CCNG1,CENPV,
CRADD,DERA,DGCR6,ETV2,GLOD4,HACL1,HOXB7,
IGBP1,LOC201651,NDFIP1,PIGH,RARS2,RNF141,TMEM219
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for ADI1


There's no related Drug.
Top
Cross referenced IDs for ADI1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas