Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 CTGF

Basic gene info.	Gene symbol	CTGF
	Gene name	connective tissue growth factor
	Synonyms	CCN2\|HCS24\|IGFBP8\|NOV2
	Cytomap	UCSC genome browser: 6q23.1
	Genomic location	chr6 :132269316-132272518
	Type of gene	protein-coding
	RefGenes	NM_001901.2,
	Ensembl id	ENSG00000118523
	Description	CCN family member 2IBP-8IGF-binding protein 8IGFBP-8hypertrophic chondrocyte-specific protein 24insulin-like growth factor-binding protein 8
	Modification date	20141207
dbXrefs	MIM : 121009
	HGNC : HGNC
	Ensembl : ENSG00000118523
	HPRD : 00412
	Vega : OTTHUMG00000015573
Protein	UniProt: P29279 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CTGF
	BioGPS: 1490
	Gene Expression Atlas: ENSG00000118523
	The Human Protein Atlas: ENSG00000118523
Pathway	NCI Pathway Interaction Database: CTGF
	KEGG: CTGF
	REACTOME: CTGF
	ConsensusPathDB
	Pathway Commons: CTGF
Metabolism	MetaCyc: CTGF
	HUMANCyc: CTGF
Regulation	Ensembl's Regulation: ENSG00000118523
	miRBase: chr6 :132,269,316-132,272,518
	TargetScan: NM_001901
	cisRED: ENSG00000118523
Context	iHOP: CTGF
	cancer metabolism search in PubMed: CTGF
	UCL Cancer Institute: CTGF
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CTGF in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	121009; gene.
Orphanet	220393; Diffuse cutaneous systemic sclerosis. 220402; Limited cutaneous systemic sclerosis.
Disease	KEGG Disease: CTGF
	MedGen: CTGF (Human Medical Genetics with Condition)
	ClinVar: CTGF
Phenotype	MGI: CTGF (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CTGF related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
CV329033	GPX7	1	289	1	53072428	53074032	CTGF	281	376	6	132270038	132270134
CN482962	KLHDC4	1	255	16	87760459	87782368	CTGF	249	612	6	132271589	132272292
CV329008	GPX7	1	289	1	53072428	53074032	CTGF	281	376	6	132270038	132270134

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr6:132270547-132270547	p.V303L	5
chr6:132271952-132271952	p.H83D	4
chr6:132271151-132271151	p.E231Q	3
chr6:132270418-132270418	p.G346R	2
chr6:132271489-132271489	p.E162K	2
chr6:132270660-132270660	p.P265L	2
chr6:132272283-132272283	p.R10R	2
chr6:132270683-132270683	p.I257I	2
chr6:132271436-132271436	p.L179L	2
chr6:132271462-132271462	p.D171Y	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3	2		5			2		1	1		2	1			1	1	1		8
# mutation	3	2		5			2		1	1		3	1			1	1	1		8
nonsynonymous SNV	3	2		4					1	1		3	1			1	1	1		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr6:132271489	p.E162K	2
chr6:132271151	p.E231Q	2
chr6:132270668	p.K343N	1
chr6:132271276	p.G216G	1
chr6:132270418	p.S338P	1
chr6:132270681	p.C213F	1
chr6:132271289	p.T322T	1
chr6:132270425	p.S207I	1
chr6:132271089	p.I195V	1
chr6:132271472	p.E311K	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA27003; -.
Organism-specific databases	CTD	1490; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB02010	connective tissue growth factor	experimental	Staurosporine

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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