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 CHST11
Basic gene info.Gene symbolCHST11
Gene namecarbohydrate (chondroitin 4) sulfotransferase 11
SynonymsC4ST|C4ST-1|C4ST1|HSA269537
CytomapUCSC genome browser: 12q
Genomic locationchr12 :104850691-105155792
Type of geneprotein-coding
RefGenesNM_001173982.1,
NM_018413.5,
Ensembl idENSG00000171310
DescriptionC4S-1IgH/CHST11 fusioncarbohydrate sulfotransferase 11chondroitin 4-O-sulfotransferase 1
Modification date20141207
dbXrefs MIM : 610128
HGNC : HGNC
Ensembl : ENSG00000171310
HPRD : 13055
Vega : OTTHUMG00000169803
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CHST11
BioGPS: 50515
Gene Expression Atlas: ENSG00000171310
The Human Protein Atlas: ENSG00000171310
PathwayNCI Pathway Interaction Database: CHST11
KEGG: CHST11
REACTOME: CHST11
ConsensusPathDB
Pathway Commons: CHST11
MetabolismMetaCyc: CHST11
HUMANCyc: CHST11
RegulationEnsembl's Regulation: ENSG00000171310
miRBase: chr12 :104,850,691-105,155,792
TargetScan: NM_001173982
cisRED: ENSG00000171310
ContextiHOP: CHST11
cancer metabolism search in PubMed: CHST11
UCL Cancer Institute: CHST11
Assigned class in ccmGDBC

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Phenotypic Information for CHST11(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CHST11
Familial Cancer Database: CHST11
* 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_SULFUR_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CHST11
MedGen: CHST11 (Human Medical Genetics with Condition)
ClinVar: CHST11
PhenotypeMGI: CHST11 (International Mouse Phenotyping Consortium)
PhenomicDB: CHST11

Mutations for CHST11
* 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
ovaryCHST11chr12104929033104929053CHST11chr12104927825104927845
ovaryCHST11chr12105052623105052643CHST11chr12105052685105052705
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 CHST11 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF926212CHST11226412104956050104956311FARP1248329139910172199101802
AI243715PPDPF7201206215332462153519CHST1120238212104851276105150789
BF922748CHST112123112105074266105074477CLPTM1L223422513361401336339
BF508216CHST111721112104893920104894114CHST1120753912104894893104895225
BI062214CHST11124512104867702104867946CHST1123039212104866579104866741
CB270023CHST118010012105120868105120888ARHGEF196220194240249542402619

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  13 1       1  
GAIN (# sample)1  1          1  
LOSS (# sample)    3 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=40)
Stat. for Synonymous SNVs
(# total SNVs=22)
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
chr12:105150997-105150997p.A159T6
chr12:105151233-105151233p.F237F3
chr12:104995690-104995690p.R42Q3
chr12:105151047-105151047p.R175R2
chr12:105150990-105150990p.H156H2
chr12:105150991-105150991p.V157I2
chr12:105151089-105151089p.F189F2
chr12:105151516-105151516p.E332K2
chr12:104995735-104995735p.R57Q2
chr12:105151183-105151183p.R221W2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample24 12  3    2511 6317
# mutation24 11  3    2511 6319
nonsynonymous SNV12 6  3     3 1 52 7
synonymous SNV12 5       221  1112
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
chr12:105150997p.A154T,CHST114
chr12:105151233p.F232F,CHST113
chr12:105150990p.H151H,CHST112
chr12:105150791p.R128Q,CHST111
chr12:105151427p.R214H,CHST111
chr12:105150996p.L331L,CHST111
chr12:105151226p.L129L,CHST111
chr12:105150871p.R216W,CHST111
chr12:105151459p.N337K,CHST111
chr12:105150891p.T134T,CHST111

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 CHST11 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 CHST11

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

ADAM19,ADCY7,ARPC2,CD86,CHST11,DSE,EMR2,
IL15RA,IL21R,PPP1R18,LAIR1,LCP2,LILRB1,LILRB2,
LYN,MSN,NCF2,PDCD1LG2,PRDM1,SLAMF8,SLC7A7
ADAM8,ARHGAP30,ARHGAP9,CD300LF,CD37,CHST11,CSF2RB,
GPR132,IL2RG,IL4I1,KLHL6,LILRB1,LPXN,MYO1G,
POU2F2,RHOF,SASH3,SEL1L3,SEMA7A,SPN,WDFY4

ADAM12,BICC1,CHST11,COL5A2,COL6A1,COL6A2,FRMD6,
GPC6,GPR68,INHBA,LILRB2,MAFB,MYO5A,NRP1,
NRP2,PDCD1LG2,RUNX2,SNAI2,TIMP2,VCAN,ZEB2
BASP1,C17orf96,RTP5,CHST11,CLSTN3,HAUS5,KIAA0922,
LIMK1,MSC,ORAI2,PIP4K2A,POU2AF1,RELT,RFTN1,
RHBDF2,S1PR2,SH2D3C,SLC7A5,TESC,TRAF1,WIPF1
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 CHST11


There's no related Drug.
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Cross referenced IDs for CHST11
* 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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