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 symbolCOL4A3BP
Gene namecollagen, type IV, alpha 3 (Goodpasture antigen) binding protein
SynonymsCERT|CERTL|GPBP|STARD11
CytomapUCSC genome browser: 5q13.3
Genomic locationchr5 :74666927-74807806
Type of geneprotein-coding
RefGenesNM_001130105.1,
NM_005713.2,NM_031361.2,
Ensembl idENSG00000113163
DescriptionStAR-related lipid transfer (START) domain containing 11ceramide transfer proteinceramide transportercollagen type IV alpha-3-binding proteinhCERTlipid-transfer protein CERTL
Modification date20141207
dbXrefs MIM : 604677
HGNC : HGNC
Ensembl : ENSG00000113163
HPRD : 05246
Vega : OTTHUMG00000102068
ProteinUniProt: Q9Y5P4
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_COL4A3BP
BioGPS: 10087
Gene Expression Atlas: ENSG00000113163
The Human Protein Atlas: ENSG00000113163
PathwayNCI Pathway Interaction Database: COL4A3BP
KEGG: COL4A3BP
REACTOME: COL4A3BP
ConsensusPathDB
Pathway Commons: COL4A3BP
MetabolismMetaCyc: COL4A3BP
HUMANCyc: COL4A3BP
RegulationEnsembl's Regulation: ENSG00000113163
miRBase: chr5 :74,666,927-74,807,806
TargetScan: NM_001130105
cisRED: ENSG00000113163
ContextiHOP: COL4A3BP
cancer metabolism search in PubMed: COL4A3BP
UCL Cancer Institute: COL4A3BP
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of COL4A3BP in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 604677; gene.
604677; gene.
Orphanet
DiseaseKEGG Disease: COL4A3BP
MedGen: COL4A3BP (Human Medical Genetics with Condition)
ClinVar: COL4A3BP
PhenotypeMGI: COL4A3BP (International Mouse Phenotyping Consortium)
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.

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 COL4A3BP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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          2      
GAIN (# sample)          1      
LOSS (# sample)          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=5

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check002.gifSomatic 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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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
chr5:74676952-74676952p.G564G3
chr5:74675210-74675210p.Y612Y3
chr5:74685495-74685495p.Q402Q2
chr5:74680490-74680490p.I489V2
chr5:74721264-74721264p.R173G2
chr5:74676936-74676936p.R570G2
chr5:74681746-74681746p.D466D2
chr5:74681788-74681788p.G452G2
chr5:74685443-74685443p.L420V2
chr5:74801860-74801860p.E60*1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  12  6 2  13   55 5
# mutation2  10  6 2  13   55 5
nonsynonymous SNV1  5  4 2  13   43 3
synonymous SNV1  5  2         12 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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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
chr5:74676952p.D440D,COL4A3BP3
chr5:74681746p.Y586Y,COL4A3BP3
chr5:74675210p.G538G,COL4A3BP3
chr5:74681788p.G426G,COL4A3BP2
chr5:74721304p.M164I,COL4A3BP1
chr5:74807074p.V427I,COL4A3BP1
chr5:74695192p.E159D,COL4A3BP1
chr5:74722212p.S147C,COL4A3BP1
chr5:74676954p.S144S,COL4A3BP1
chr5:74696051p.P417H,COL4A3BP1

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 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

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

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
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 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



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