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 CTGF
Basic gene info.Gene symbolCTGF
Gene nameconnective tissue growth factor
SynonymsCCN2|HCS24|IGFBP8|NOV2
CytomapUCSC genome browser: 6q23.1
Genomic locationchr6 :132269316-132272518
Type of geneprotein-coding
RefGenesNM_001901.2,
Ensembl idENSG00000118523
DescriptionCCN family member 2IBP-8IGF-binding protein 8IGFBP-8hypertrophic chondrocyte-specific protein 24insulin-like growth factor-binding protein 8
Modification date20141207
dbXrefs MIM : 121009
HGNC : HGNC
Ensembl : ENSG00000118523
HPRD : 00412
Vega : OTTHUMG00000015573
ProteinUniProt: P29279
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CTGF
BioGPS: 1490
Gene Expression Atlas: ENSG00000118523
The Human Protein Atlas: ENSG00000118523
PathwayNCI Pathway Interaction Database: CTGF
KEGG: CTGF
REACTOME: CTGF
ConsensusPathDB
Pathway Commons: CTGF
MetabolismMetaCyc: CTGF
HUMANCyc: CTGF
RegulationEnsembl's Regulation: ENSG00000118523
miRBase: chr6 :132,269,316-132,272,518
TargetScan: NM_001901
cisRED: ENSG00000118523
ContextiHOP: CTGF
cancer metabolism search in PubMed: CTGF
UCL Cancer Institute: CTGF
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CTGF in cancer cell metabolism1. Lu H, Kojima K, Battula VL, Korchin B, Shi Y, et al. (2014) Targeting connective tissue growth factor (CTGF) in acute lymphoblastic leukemia preclinical models: anti-CTGF monoclonal antibody attenuates leukemia growth. Ann Hematol 93: 485-492. doi: 10.1007/s00277-013-1939-2. pmid: 3948212. go to article
2. Gao YB, Xiang ZL, Zhou LY, Wu ZF, Fan J, et al. (2013) Enhanced production of CTGF and IL-11 from highly metastatic hepatoma cells under hypoxic conditions: an implication of hepatocellular carcinoma metastasis to bone. J Cancer Res Clin Oncol 139: 669-679. doi: 10.1007/s00432-012-1370-4. go to article
3. Uriarte I, Latasa MU, Carotti S, Fernandez-Barrena MG, Garcia-Irigoyen O, et al. (2015) Ileal FGF15 contributes to fibrosis-associated hepatocellular carcinoma development. Int J Cancer 136: 2469-2475. doi: 10.1002/ijc.29287. go to article

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

check002.gifOthers
OMIM 121009; gene.
Orphanet 220393; Diffuse cutaneous systemic sclerosis.
220402; Limited cutaneous systemic sclerosis.
DiseaseKEGG Disease: CTGF
MedGen: CTGF (Human Medical Genetics with Condition)
ClinVar: CTGF
PhenotypeMGI: CTGF (International Mouse Phenotyping Consortium)
PhenomicDB: CTGF

Mutations for CTGF
* 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 CTGF related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV329033GPX7128915307242853074032CTGF2813766132270038132270134
CN482962KLHDC41255168776045987782368CTGF2496126132271589132272292
CV329008GPX7128915307242853074032CTGF2813766132270038132270134

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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr6:132270547-132270547p.V303L5
chr6:132271952-132271952p.H83D4
chr6:132271151-132271151p.E231Q3
chr6:132270660-132270660p.P265L2
chr6:132272283-132272283p.R10R2
chr6:132270683-132270683p.I257I2
chr6:132271436-132271436p.L179L2
chr6:132270418-132270418p.G346R2
chr6:132271489-132271489p.E162K2
chr6:132270449-132270449p.I335I1

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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
# sample32 5  2 11 21  111 8
# mutation32 5  2 11 31  111 8
nonsynonymous SNV32 4    11 31  111 5
synonymous SNV   1  2            3
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
chr6:132271489p.E162K2
chr6:132271151p.E231Q2
chr6:132270523p.Y279Y1
chr6:132271165p.Y279H1
chr6:132270531p.R142C1
chr6:132271177p.I262I1
chr6:132270533p.R258H1
chr6:132271194p.K251N1
chr6:132270605p.E248K1
chr6:132271204p.M348V1

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 CTGF 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 CTGF

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

C2orf40,COL11A2,CTGF,CYP26B1,CYR61,EGR1,FERMT2,
FGF7,FNDC1,FSTL1,ISM1,LATS2,MAGEL2,MSRB3,
NAP1L3,NPR2,PENK,PTRF,RECK,SEMA3D,ZNF469
MB21D2,CHSY1,CSRNP1,CTGF,CYR61,DDX5,FOSL1,
GADD45A,GPR3,ITPRIP,KLF6,LDLR,MAFF,MCL1,
NEDD9,PER2,RHOU,SERPINE1,SIK1,TIPARP,WEE1

MEDAG,CCDC80,CTGF,CYR61,DLC1,FBN1,FGF1,
GDF6,KCNE4,LHFP,LTBP2,MMP19,NOX4,PKD2,
PTRF,SERPINF1,THBS1,THBS2,VCAN,VGLL3,VIM
ADAMTS1,ADAMTS4,AGR2___C11orf96,CEBPB,CHSY1,CSRNP1,CTGF,
CYR61,EGR4,GPR4,HEYL,ITPRIP,JAG1,KLHL15,
MMP19,PHLDA1,SCARNA9,SERPINE1,SF3B4,THBS1,ZFP36
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 CTGF
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA27003; -.
Organism-specific databasesCTD 1490; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02010connective tissue growth factorexperimentalStaurosporine


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Cross referenced IDs for CTGF
* 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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