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 COL4A3BP

Basic gene info.	Gene symbol	COL4A3BP
	Gene name	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein
	Synonyms	CERT\|CERTL\|GPBP\|STARD11
	Cytomap	UCSC genome browser: 5q13.3
	Genomic location	chr5 :74666927-74807806
	Type of gene	protein-coding
	RefGenes	NM_001130105.1, NM_005713.2,NM_031361.2,
	Ensembl id	ENSG00000113163
	Description	StAR-related lipid transfer (START) domain containing 11ceramide transfer proteinceramide transportercollagen type IV alpha-3-binding proteinhCERTlipid-transfer protein CERTL
	Modification date	20141207
dbXrefs	MIM : 604677
	HGNC : HGNC
	Ensembl : ENSG00000113163
	HPRD : 05246
	Vega : OTTHUMG00000102068
Protein	UniProt: Q9Y5P4 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_COL4A3BP
	BioGPS: 10087
	Gene Expression Atlas: ENSG00000113163
	The Human Protein Atlas: ENSG00000113163
Pathway	NCI Pathway Interaction Database: COL4A3BP
	KEGG: COL4A3BP
	REACTOME: COL4A3BP
	ConsensusPathDB
	Pathway Commons: COL4A3BP
Metabolism	MetaCyc: COL4A3BP
	HUMANCyc: COL4A3BP
Regulation	Ensembl's Regulation: ENSG00000113163
	miRBase: chr5 :74,666,927-74,807,806
	TargetScan: NM_001130105
	cisRED: ENSG00000113163
Context	iHOP: COL4A3BP
	cancer metabolism search in PubMed: COL4A3BP
	UCL Cancer Institute: COL4A3BP
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of COL4A3BP in cancer cell metabolism	1. Heering J, Weis N, Holeiter M, Neugart F, Staebler A, et al. (2012) Loss of the ceramide transfer protein augments EGF receptor signaling in breast cancer. Cancer Res 72: 2855-2866. doi: 10.1158/0008-5472.CAN-11-3069. go to article 2. Rao RP, Scheffer L, Srideshikan SM, Parthibane V, Kosakowska-Cholody T, et al. (2014) Ceramide transfer protein deficiency compromises organelle function and leads to senescence in primary cells. PLoS One 9: e92142. doi: 10.1371/journal.pone.0092142. pmid: 3958450. go to article 3. Lee AJ, Roylance R, Sander J, Gorman P, Endesfelder D, et al. (2012) CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid-specific cancer cell death through autophagy induction. J Pathol 226: 482-494. doi: 10.1002/path.2998. go to article 4. Hullin-Matsuda F, Tomishige N, Sakai S, Ishitsuka R, Ishii K, et al. (2012) Limonoid compounds inhibit sphingomyelin biosynthesis by preventing CERT protein-dependent extraction of ceramides from the endoplasmic reticulum. J Biol Chem 287: 24397-24411. doi: 10.1074/jbc.M112.356733. pmid: 3397866. go to article 5. Swanton C, Marani M, Pardo O, Warne PH, Kelly G, et al. (2007) Regulators of mitotic arrest and ceramide metabolism are determinants of sensitivity to paclitaxel and other chemotherapeutic drugs. Cancer Cell 11: 498-512. doi: 10.1016/j.ccr.2007.04.011. go to article

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Phenotypic Information for COL4A3BP(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: COL4A3BP
	Familial Cancer Database: COL4A3BP

* 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_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	604677; gene. 604677; gene.
Orphanet
Disease	KEGG Disease: COL4A3BP
	MedGen: COL4A3BP (Human Medical Genetics with Condition)
	ClinVar: COL4A3BP
Phenotype	MGI: COL4A3BP (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: COL4A3BP

Mutations for COL4A3BP

* 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 COL4A3BP related fusion information.

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

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=32)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr5:74675210-74675210	p.Y612Y	3
chr5:74676952-74676952	p.G564G	3
chr5:74685495-74685495	p.Q402Q	2
chr5:74680490-74680490	p.I489V	2
chr5:74721264-74721264	p.R173G	2
chr5:74676936-74676936	p.R570G	2
chr5:74681746-74681746	p.D466D	2
chr5:74681788-74681788	p.G452G	2
chr5:74685443-74685443	p.L420V	2
chr5:74698830-74698830	p.A328A	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=3

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	2			12			6		2			1	3				5	5		5
# mutation	2			10			6		2			1	3				5	5		5
nonsynonymous SNV	1			5			4		2			1	3				4	3		3
synonymous SNV	1			5			2										1	2		2

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
chr5:74675210	p.Y586Y,COL4A3BP	3
chr5:74676952	p.G538G,COL4A3BP	3
chr5:74681746	p.D440D,COL4A3BP	3
chr5:74681788	p.G426G,COL4A3BP	2
chr5:74801891	p.G363G,COL4A3BP	1
chr5:74685443	p.Y55D,COL4A3BP	1
chr5:74712780	p.T351I,COL4A3BP	1
chr5:74675245	p.N49N,COL4A3BP	1
chr5:74801935	p.E575Q,COL4A3BP	1
chr5:74685485	p.L316L,COL4A3BP	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 COL4A3BP 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 COL4A3BP

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


AFF4,AGGF1,APC,COL4A3BP,DMXL1,ERBB2IP,FBXL17, FCHO2,IPO11,LYSMD3,MFAP3,PGGT1B,PJA2,POLK, SCAMP1,SLC25A46,SLC30A5,SMAD5,TNPO1,TRIM23,ZFYVE16	ACER3,ANO6,GPATCH11,COL4A3BP,CRYBG3,DDHD2,EIF4EBP2, FERMT2,GNAI1,JAK1,MDFIC,MTMR10,PCYOX1,PDE8A, PEX19,PPP2R5A,RRAGC,SIK2,SLC25A16,SORT1,UBA2

AGGF1,AP3B1,BDP1,CHD1,CNOT6,COL4A3BP,DHX29, DMXL1,ELL2,FBXW11,LHFPL2,LNPEP,LYSMD3,PHAX, PJA2,POLK,PURA,RNF145,SEC24A,TMEM167A,TRIM23	BTBD7,COL4A3BP,DDX6,DNAJC13,FBXO11,FBXW11,GLG1, IPO8,JAK1,GLTSCR1L,KIAA0430,KIDINS220,KIF1B,LOC647979, MKLN1,KAT7,PHF3,PUM2,RPRD2,SIN3A,TNRC6B

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 COL4A3BP

There's no related Drug.

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Cross referenced IDs for COL4A3BP

* 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