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 CASC3

Basic gene info.	Gene symbol	CASC3
	Gene name	cancer susceptibility candidate 3
	Synonyms	BTZ\|MLN51
	Cytomap	UCSC genome browser: 17q21.1
	Genomic location	chr17 :38296506-38328431
	Type of gene	protein-coding
	RefGenes	NM_007359.4,
	Ensembl id	ENSG00000108349
	Description	MLN 51barentszcancer susceptibility candidate gene 3 proteinmetastatic lymph node 51metastatic lymph node gene 51 proteinprotein CASC3protein barentsz
	Modification date	20141207
dbXrefs	MIM : 606504
	HGNC : HGNC
	Ensembl : ENSG00000108349
	HPRD : 16225
	Vega : OTTHUMG00000133323
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CASC3
	BioGPS: 22794
	Gene Expression Atlas: ENSG00000108349
	The Human Protein Atlas: ENSG00000108349
Pathway	NCI Pathway Interaction Database: CASC3
	KEGG: CASC3
	REACTOME: CASC3
	ConsensusPathDB
	Pathway Commons: CASC3
Metabolism	MetaCyc: CASC3
	HUMANCyc: CASC3
Regulation	Ensembl's Regulation: ENSG00000108349
	miRBase: chr17 :38,296,506-38,328,431
	TargetScan: NM_007359
	cisRED: ENSG00000108349
Context	iHOP: CASC3
	cancer metabolism search in PubMed: CASC3
	UCL Cancer Institute: CASC3
Assigned class in ccmGDB	C

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Phenotypic Information for CASC3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CASC3
	Familial Cancer Database: CASC3

* 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_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: CASC3
	MedGen: CASC3 (Human Medical Genetics with Condition)
	ClinVar: CASC3
Phenotype	MGI: CASC3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CASC3

Mutations for CASC3

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	CASC3	chr17	38302338	38302358		chr17	76252053	76252073
ovary	CASC3	chr17	38309671	38309691	CASC3	chr17	38314443	38314463

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CASC3 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
AI206204	IQCD	5	174	12	113633251	113633420	CASC3	167	460	17	38327416	38327709
BF750860	CASC3	10	67	17	38328074	38328133	CTDSP1	62	431	2	219270222	219270592
AW377350	CASC3	8	145	17	38323498	38323637	EXOSC10	145	643	1	11140178	11140691
AW377331	CASC3	11	148	17	38323498	38323637	EXOSC10	146	611	1	11140175	11140646
AA190703	CASC3	1	106	17	38327833	38327938	CASC3	105	389	17	38327907	38328188
AW377333	CASC3	10	148	17	38323497	38323637	EXOSC10	145	645	1	11140175	11140691

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=28)	Stat. for Synonymous SNVs (# total SNVs=17)

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
chr17:38324586-38324586	p.V627V	3
chr17:38324639-38324639	p.P645L	3
chr17:38325584-38325584	p.S658L	3
chr17:38319064-38319064	p.S232F	3
chr17:38296830-38296830	p.S10L	3
chr17:38324513-38324513	p.P603L	3
chr17:38325681-38325681	p.I690I	3
chr17:38319959-38319959	p.G337G	3
chr17:38319117-38319117	p.P250S	2
chr17:38323834-38323834	p.I540I	2

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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	3	1	1	4			1		2	1		6		1	1		7	4	1	9
# mutation	3	1	1	4			1		2	1		6		1	1		8	4	1	9
nonsynonymous SNV	2	1	1	1			1					3		1			6	3		7
synonymous SNV	1			3					2	1		3			1		2	1	1	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
chr17:38319959	p.G337G	3
chr17:38318284	p.V162V	2
chr17:38319010	p.E118K	1
chr17:38320310	p.R338R	1
chr17:38297832	p.R682Q	1
chr17:38324637	p.T138T	1
chr17:38319103	p.R409I	1
chr17:38320314	p.P692P	1
chr17:38297833	p.D150D	1
chr17:38325581	p.E422K	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 CASC3 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 CASC3

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


CASC3,CDC6,CDK12,ERBB2,FBXL20,GRB7,LOC90110, MED1,MED24,MSL1,NR1D1,ORMDL3,PGAP3,PSMD3, RAPGEFL1,RARA,SMARCE1,STARD3,THRA,TOP2A,WIPF2	ASB7,CASC3,CEP57,CUL4B,DHX40,DIP2B,KIAA0430, MBTD1,PLEKHA5,PUM2,SAV1,TRMT5,TUG1,WDR48, ZBTB26,ZFP90,ZMYM4,ZNF345,ZNF512,ZNF616,ZNF84

MIEN1,CASC3,CDC6,ERBB2,GRB7,MED24,MSL1, NDUFC2,ORMDL3,PGAP3,PPP1R1B,PSMD3,RAPGEFL1,RARA, SMARCE1,SNX32,TCAP,THRA,TOP2A,UGT1A8,WIPF2	VSTM4,CASC3,CRTC3,DIP2C,DSTYK,EVC,FRMD4A, FYCO1,GLI2,LRIG1,NFIC,NFIX,NPR2,NR2F2, PIP4K2B,RUNX1T1,STAT5B,TRPS1,WDR35,ZBTB4,ZFYVE20

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 CASC3

There's no related Drug.

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Cross referenced IDs for CASC3

* 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