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 CHIT1
Basic gene info.Gene symbolCHIT1
Gene namechitinase 1 (chitotriosidase)
SynonymsCHI3|CHIT|CHITD
CytomapUCSC genome browser: 1q32.1
Genomic locationchr1 :203185206-203198860
Type of geneprotein-coding
RefGenesNM_001256125.1,
NM_001270509.1,NM_003465.2,NR_045784.1,NR_045785.1,
Ensembl idENSG00000133063
Descriptionchitotriosidase-1plasma methylumbelliferyl tetra-N-acetylchitotetraoside hydrolase
Modification date20141207
dbXrefs MIM : 600031
HGNC : HGNC
Ensembl : ENSG00000133063
HPRD : 02494
Vega : OTTHUMG00000042126
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CHIT1
BioGPS: 1118
Gene Expression Atlas: ENSG00000133063
The Human Protein Atlas: ENSG00000133063
PathwayNCI Pathway Interaction Database: CHIT1
KEGG: CHIT1
REACTOME: CHIT1
ConsensusPathDB
Pathway Commons: CHIT1
MetabolismMetaCyc: CHIT1
HUMANCyc: CHIT1
RegulationEnsembl's Regulation: ENSG00000133063
miRBase: chr1 :203,185,206-203,198,860
TargetScan: NM_001256125
cisRED: ENSG00000133063
ContextiHOP: CHIT1
cancer metabolism search in PubMed: CHIT1
UCL Cancer Institute: CHIT1
Assigned class in ccmGDBC

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Phenotypic Information for CHIT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CHIT1
Familial Cancer Database: CHIT1
* 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_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: CHIT1
MedGen: CHIT1 (Human Medical Genetics with Condition)
ClinVar: CHIT1
PhenotypeMGI: CHIT1 (International Mouse Phenotyping Consortium)
PhenomicDB: CHIT1

Mutations for CHIT1
* 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 CHIT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP305867NAA5014133113442329113465007CHIT14145801203194920203198796

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 # 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)

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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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=56)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr1:203186947-203186947p.A359G8
chr1:203186950-203186950p.W358*5
chr1:203194186-203194186p.G102S4
chr1:203186950-203186951p.V357_W358ins*4
chr1:203192738-203192738p.S122*2
chr1:203194880-203194880p.F58F2
chr1:203186892-203186892p.L377L2
chr1:203194936-203194936p.R40C2
chr1:203188447-203188447p.W309*2
chr1:203192643-203192643p.R154C2

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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
# sample4  8  213 1671  154 8
# mutation4  8  213 1671  154 8
nonsynonymous SNV3  6  1 3 145   113 7
synonymous SNV1  2  11   221  41 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
chr1:203194880p.F58F,CHIT12
chr1:203194936p.T153T,CHIT12
chr1:203192352p.R40C,CHIT12
chr1:203186215p.V202V,CHIT11
chr1:203192633p.S103W,CHIT11
chr1:203194802p.K329N,CHIT11
chr1:203188818p.G197D,CHIT11
chr1:203186021p.N102I,CHIT11
chr1:203191413p.E319E,CHIT11
chr1:203186253p.G197C,CHIT11

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 CHIT1 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 CHIT1

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

APOC1,CD68,CDH9,CHIT1,CTSS,DPEP2,FGR,
FOXB2,GM2A,GPR150,HTRA4,ITGAX,ITGB2,LILRA2,
LILRB4,LIPA,NCF2,PILRA,TM4SF19,DCSTAMP,TMEM114
ADAM8,APOC1,APOC2,ATP6V0D2,BIRC7,CELA1,CHIT1,
DEC1,DNAJC5B,HS3ST2,HTRA4,ITGAD,LILRA4,MGAM,
NKX2-6,PKD2L1,PRAMEF22,SCARNA11,SCN10A,SDS,SNORA27

ACP5,APOC1,APOE,CHI3L1,CHIT1,DNAJC5B,GPNMB,
HAMP,HK3,HTRA4,ITGB2,LIPA,LOC653786,OSCAR,
PRAM1,RAB42,SPP1,TM4SF19,DCSTAMP,TREM2,VSIG4
ACTBL2,CCL18,CHIT1,DEFB103B,DEFB4A,FAM74A1,FAM92A1P2,
FLJ25758,HS3ST2,HTRA4,KRT6B,KRTAP13-1,LY6D,MMP10,
OR1J1,OR1J2,PRAMEF12,RBMXL3,TM4SF19,TRIM42,XKRY2
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 CHIT1
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
DB03109chitinase 1 (chitotriosidase)experimentalN-Acetyl-D-Allosamine
DB03539chitinase 1 (chitotriosidase)experimental2-(Acetylamino)-2-Deoxy-6-O-Methyl-Alpha-D-Allopyranose
DB03632chitinase 1 (chitotriosidase)experimentalArgifin
DB04350chitinase 1 (chitotriosidase)experimentalArgadin
DB04404chitinase 1 (chitotriosidase)experimentalAllosamizoline


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Cross referenced IDs for CHIT1
* 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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