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 ARSE
Basic gene info.Gene symbolARSE
Gene namearylsulfatase E (chondrodysplasia punctata 1)
SynonymsASE|CDPX|CDPX1|CDPXR
CytomapUCSC genome browser: Xp22.3
Genomic locationchrX :2852672-2882494
Type of geneprotein-coding
RefGenesNM_000047.2,
NM_001282628.1,NM_001282631.1,
Ensembl idENSG00000157399
Descriptionarylsulfatase E
Modification date20141219
dbXrefs MIM : 300180
HGNC : HGNC
Ensembl : ENSG00000157399
HPRD : 02171
Vega : OTTHUMG00000137358
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ARSE
BioGPS: 415
Gene Expression Atlas: ENSG00000157399
The Human Protein Atlas: ENSG00000157399
PathwayNCI Pathway Interaction Database: ARSE
KEGG: ARSE
REACTOME: ARSE
ConsensusPathDB
Pathway Commons: ARSE
MetabolismMetaCyc: ARSE
HUMANCyc: ARSE
RegulationEnsembl's Regulation: ENSG00000157399
miRBase: chrX :2,852,672-2,882,494
TargetScan: NM_000047
cisRED: ENSG00000157399
ContextiHOP: ARSE
cancer metabolism search in PubMed: ARSE
UCL Cancer Institute: ARSE
Assigned class in ccmGDBC

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Phenotypic Information for ARSE(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ARSE
Familial Cancer Database: ARSE
* 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
REACTOME_GLYCOSPHINGOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for ARSE
* 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 ARSE 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
There's no copy number variation information in COSMIC data for this gene.

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=41)
Stat. for Synonymous SNVs
(# total SNVs=16)
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
chr23:2861175-2861175p.D353N3
chr23:2867520-2867520p.V227I3
chr23:2867504-2867504p.L232P2
chr23:2856245-2856245p.R394C2
chr23:2852896-2852896p.L583V2
chr23:2876407-2876407p.S31S2
chr23:2873479-2873479p.T95T2
chr23:2856150-2856150p.E425E2
chr23:2873545-2873545p.G73G2
chr23:2867709-2867709p.H164Y1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 44 1 1  121 15628
# mutation13 54 1 1  121 157213
nonsynonymous SNV 2 43 1     2  14319
synonymous SNV11 11   1  1 1  1414
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
chrX:2876407p.S31S,ARSE2
chrX:2856150p.E380E,ARSE2
chrX:2873479p.T50T,ARSE2
chrX:2861135p.T226T,ARSE1
chrX:2867585p.G57V,ARSE1
chrX:2876330p.H402H,ARSE1
chrX:2854853p.T217M,ARSE1
chrX:2864051p.D32N,ARSE1
chrX:2867631p.V381A,ARSE1
chrX:2876406p.R212K,ARSE1

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 ARSE 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 ARSE

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

ARSE,CCIN,CMTM3,CMTM5,DACT3,DEPDC7,DZIP1,
FHL3,GFRA3,GPX7,KDELC1,LOC100270710,MFAP2,PODNL1,
PPAPDC1A,RNF144A,SLC38A5,THY1,TM6SF2,SYNDIG1,TPM2
ARSE,CA11,CCNJL,CDH3,CLSTN1,DTX3,EFNB3,
FZD7,HEPH,LAYN,MAGED4,MAGED4B,NUDT10,PAQR7,
RBM23,SCG5,SLC35F3,SMO,ST5,TMEM98,TRNP1

ARSD,ARSE,CTPS2,EIF1AX,FUNDC1,GEMIN8,GJB1,
GYG2,HDHD1,OFD1,PNPLA4,RBBP7,RPS4X,SLC25A6,
SLC39A5,SYAP1,TIMM17B,TINAG,TRAPPC2,TSPAN6,VIL1
ARSD,ARSE,CDK16,CHDH,CISH,COX19,GRHL2,
HDHD1,KDM5C,LENG9,MNX1,MYCL,PNPLA4,PRKX,
QARS,REEP4,REPIN1,ARHGEF28,RPS4X,ZBED9,TRAPPC2
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 ARSE
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
DB00682arylsulfatase E (chondrodysplasia punctata 1)approvedWarfarin


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Cross referenced IDs for ARSE
* 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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