Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 ACAN
Basic gene info.Gene symbolACAN
Gene nameaggrecan
SynonymsAGC1|AGCAN|CSPG1|CSPGCP|MSK16|SEDK
CytomapUCSC genome browser: 15q26.1
Genomic locationchr15 :89346673-89418585
Type of geneprotein-coding
RefGenesNM_001135.3,
NM_013227.3,
Ensembl idENSG00000157766
Descriptionaggrecan core proteincartilage-specific proteoglycan core proteinchondroitin sulfate proteoglycan core protein 1large aggregating proteoglycan
Modification date20141222
dbXrefs MIM : 155760
HGNC : HGNC
Ensembl : ENSG00000157766
HPRD : 01123
Vega : OTTHUMG00000171989
ProteinUniProt: P16112
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACAN
BioGPS: 176
Gene Expression Atlas: ENSG00000157766
The Human Protein Atlas: ENSG00000157766
PathwayNCI Pathway Interaction Database: ACAN
KEGG: ACAN
REACTOME: ACAN
ConsensusPathDB
Pathway Commons: ACAN
MetabolismMetaCyc: ACAN
HUMANCyc: ACAN
RegulationEnsembl's Regulation: ENSG00000157766
miRBase: chr15 :89,346,673-89,418,585
TargetScan: NM_001135
cisRED: ENSG00000157766
ContextiHOP: ACAN
cancer metabolism search in PubMed: ACAN
UCL Cancer Institute: ACAN
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ACAN in cancer cell metabolism1. Kim KN, Ham YM, Moon JY, Kim MJ, Jung YH, et al. (2012) Acanthoic acid induces cell apoptosis through activation of the p38 MAPK pathway in HL-60 human promyelocytic leukaemia. Food Chem 135: 2112-2117. doi: 10.1016/j.foodchem.2012.05.067. go to article
2. Asai N, Ohkawara B, Ito M, Masuda A, Ishiguro N, et al. (2014) LRP4 induces extracellular matrix productions and facilitates chondrocyte differentiation. Biochem Biophys Res Commun 451: 302-307. doi: 10.1016/j.bbrc.2014.07.125. go to article

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

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

Mutations for ACAN
* 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
breastACANchr158936295389362953FANCIchr158982588689825886
NSACANchr158941660589416605CRTC3chr159112785191127851
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 ACAN related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG924790CCDC9786158194182624741826319ACAN157603158941800989418455
BG900931ACAN85191158940156289401668ACAN186680158940165589402149
BF061357FBLN711382112945649112945786ACAN133407158940168589401959

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 # sample2   211       1  
GAIN (# sample)2    1        1  
LOSS (# sample)    2 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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=233)
Stat. for Synonymous SNVs
(# total SNVs=74)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=2)

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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
chr15:89400023-89400023p.T1289A5
chr15:89398605-89398605p.S930I4
chr15:89402051-89402051p.I1965V4
chr15:89415247-89415247p.D2259E4
chr15:89399111-89399111p.A1099T4
chr15:89402035-89402035p.V1959V3
chr15:89382102-89382102p.R93R3
chr15:89398825-89398825p.T1003T3
chr15:89391161-89391161p.R542W3
chr15:89386810-89386810p.V328I3

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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
# sample1041267 11 101145132234921115
# mutation1141288 11 91149142238723126
nonsynonymous SNV63 245 10 4  39121135419115
synonymous SNV51143 1 51110211 334 11
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
chr15:89401084p.I139I,ACAN2
chr15:89401708p.G952E,ACAN2
chr15:89401133p.R93R,ACAN2
chr15:89401939p.V328I,ACAN2
chr15:89391161p.S1756S,ACAN2
chr15:89400924p.F2041F,ACAN2
chr15:89382102p.T335M,ACAN2
chr15:89386810p.L1773I,ACAN2
chr15:89386832p.V637I,ACAN2
chr15:89398671p.R542W,ACAN2

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 ACAN 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 ACAN

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

ACAN,NPR3,CLEC18A,ENPEP,FXYD4,HCN1,LCTL,
NOS2,PANX3,PGM5P2,PHOSPHO1,PMP2,PRELP,PRKCA,
PRSS54,SLC6A18,SPINT4,TRPV4,USH1G,WWP2,ZBTB32
ACAN,ADARB1,ANKRD34C,CACNA1H,DGKG,FHL5,GPR20,
GPR21,HTR1B,ITGA8,ITIH3,KCNA5,MRVI1,MYH11,
MYOCD,OR51E2,P2RX1,SCUBE3,SUSD5,TGM2,WFDC1

ACAN,ADAMTS7,AJAP1,CD93,CDH6,COL15A1,COL4A1,
COL4A2,GPR116,GPR124,GPR4,KDR,MCAM,NID2,
NOTCH3,NOVA2,PCDH12,PCDH17,TBX2,TBXA2R,TRPC6
ACAN,AWAT2,ADM5,C20orf141,NCOR1P1,BPIFA2,CLEC4G,
GPX5,ITIH3,KPRP,LCE2C,MEPE,CHODL-AS1,NOTCH3,
OBP2A,OR2D2,PGLYRP3,SNORA79,STEAP4,TRIM6-TRIM34,ZSWIM2
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 ACAN
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
DB02255aggrecanexperimentalGM6001


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Cross referenced IDs for ACAN
* 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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