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 AKR1C4
Basic gene info.Gene symbolAKR1C4
Gene namealdo-keto reductase family 1, member C4
Synonyms3-alpha-HSD|C11|CDR|CHDR|DD-4|DD4|HAKRA
CytomapUCSC genome browser: 10p15.1
Genomic locationchr10 :5238797-5260910
Type of geneprotein-coding
RefGenesNM_001818.3,
Ensembl idENSG00000266359
Description3-alpha-HSD1aldo-keto reductase family 1 member C4chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4dihydrodiol dehydrogenase isozyme DD4type I 3-alpha-hydroxysteroid dehydrogenase
Modification date20141211
dbXrefs MIM : 600451
HGNC : HGNC
Ensembl : ENSG00000198610
HPRD : 07040
Vega : OTTHUMG00000017591
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AKR1C4
BioGPS: 1109
Gene Expression Atlas: ENSG00000266359
The Human Protein Atlas: ENSG00000266359
PathwayNCI Pathway Interaction Database: AKR1C4
KEGG: AKR1C4
REACTOME: AKR1C4
ConsensusPathDB
Pathway Commons: AKR1C4
MetabolismMetaCyc: AKR1C4
HUMANCyc: AKR1C4
RegulationEnsembl's Regulation: ENSG00000266359
miRBase: chr10 :5,238,797-5,260,910
TargetScan: NM_001818
cisRED: ENSG00000266359
ContextiHOP: AKR1C4
cancer metabolism search in PubMed: AKR1C4
UCL Cancer Institute: AKR1C4
Assigned class in ccmGDBC

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Phenotypic Information for AKR1C4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: AKR1C4
Familial Cancer Database: AKR1C4
* 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_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: AKR1C4
MedGen: AKR1C4 (Human Medical Genetics with Condition)
ClinVar: AKR1C4
PhenotypeMGI: AKR1C4 (International Mouse Phenotyping Consortium)
PhenomicDB: AKR1C4

Mutations for AKR1C4
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows AKR1C4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample1       2        
GAIN (# sample)1       2        
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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=48)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr10:5247796-5247796p.E149G7
chr10:5238849-5238849p.R7C4
chr10:5238875-5238875p.F15F3
chr10:5260682-5260682p.L311V3
chr10:5254979-5254979p.L235I3
chr10:5254591-5254591p.P195S3
chr10:5255064-5255064p.R263H2
chr10:5248263-5248263p.G158E2
chr10:5254676-5254676p.R223Q2
chr10:5255081-5255081p.A269T2

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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=7

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 122 2 1  412  85 6
# mutation12 72 2 1  412  85 7
nonsynonymous SNV12 62 2 1  312  75 6
synonymous SNV   1       1    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])

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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
chr10:5247796p.E149G7
chr10:5254676p.F139F2
chr10:5247730p.G158A2
chr10:5247767p.R223Q2
chr10:5254979p.L235I2
chr10:5248263p.T127M2
chr10:5254588p.D12N1
chr10:5258755p.S271R1
chr10:5238879p.F15F1
chr10:5246355p.T147T1

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 AKR1C4 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 AKR1C4

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

AHSG,AKR1C4,ANGPTL3,APCS,APOA2,APOA4,APOC3,
C8A,C9,CRP,F2,F9,FABP1,FGF23,
ITIH1,PLG,SERPINA7,SERPINC1,SLC17A2,SULT2A1,TM4SF5
AKAP12,AKR1C1,AKR1C3,AKR1C4,C8orf34,CALM1,CAV1,
CRH,DMGDH,EHBP1,FAM149A,GALNT13,GLYAT,HHIP,
MCAM,MPZ,RBPMS2,RFTN1,SPARC,SPATA9,TBX4

AKR1C3,AKR1C4,BST1,CAB39L,CLN5,CST1,CST4,
DEFB104A,ENPP2,HAO2,LOC284661,LRRC69,MAL2,MED4,
MT3,N6AMT2,OR10X1,S100Z,SAP18,SLC12A1,UNC5D
AADAC,ABCC2,AGXT2,AKR1C4,ERICH4,CYP2D6,DAB1,
KCNJ13,LOC285733,MIR31HG,MGAM,MME,MS4A10,NAT8,
PDZD7,RBP3,SHBG,SLC13A1,SOAT2,SULT2A1,TMPRSS15
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 AKR1C4
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157aldo-keto reductase family 1, member C4approved; nutraceuticalNADH
DB00145aldo-keto reductase family 1, member C4approved; nutraceuticalGlycine


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Cross referenced IDs for AKR1C4
* 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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