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 IDH3B

Basic gene info.	Gene symbol	IDH3B
	Gene name	isocitrate dehydrogenase 3 (NAD+) beta
	Synonyms	H-IDHB\|RP46
	Cytomap	UCSC genome browser: 20p13
	Genomic location	chr20 :2639660-2644865
	Type of gene	protein-coding
	RefGenes	NM_001258384.1, NM_006899.3,NM_174855.2,NM_174856.1,
	Ensembl id	ENSG00000101365
	Description	NAD(+)-specific ICDH subunit betaNAD+-specific ICDHNAD+-specific isocitrate dehydrogenase b subunitNAD+-specific isocitrate dehydrogenase betaisocitrate dehydrogenase [NAD] subunit beta, mitochondrialisocitrate dehydrogenase, NAD(+)-specific, mitocho
	Modification date	20141219
dbXrefs	MIM : 604526
	HGNC : HGNC
	Ensembl : ENSG00000101365
	HPRD : 05163
	Vega : OTTHUMG00000031699
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_IDH3B
	BioGPS: 3420
	Gene Expression Atlas: ENSG00000101365
	The Human Protein Atlas: ENSG00000101365
Pathway	NCI Pathway Interaction Database: IDH3B
	KEGG: IDH3B
	REACTOME: IDH3B
	ConsensusPathDB
	Pathway Commons: IDH3B
Metabolism	MetaCyc: IDH3B
	HUMANCyc: IDH3B
Regulation	Ensembl's Regulation: ENSG00000101365
	miRBase: chr20 :2,639,660-2,644,865
	TargetScan: NM_001258384
	cisRED: ENSG00000101365
Context	iHOP: IDH3B
	cancer metabolism search in PubMed: IDH3B
	UCL Cancer Institute: IDH3B
Assigned class in ccmGDB	C

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Phenotypic Information for IDH3B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: IDH3B
	Familial Cancer Database: IDH3B

* 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_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

Others
OMIM
Orphanet
Disease	KEGG Disease: IDH3B
	MedGen: IDH3B (Human Medical Genetics with Condition)
	ClinVar: IDH3B
Phenotype	MGI: IDH3B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: IDH3B

Mutations for IDH3B

* 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 IDH3B 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
BG991562	IDH3B	27	237	20	2641424	2644189	JUP	238	427	17	39740115	39776976
AF023265	UBAC2	1	87	13	100038542	100038628	IDH3B	79	1278	20	2639041	2644835
BI015407	PSAP	16	170	10	73580052	73581743	IDH3B	166	243	20	2640724	2640801
BQ366218	MYT1L	242	263	2	2242110	2242131	IDH3B	249	680	20	2639303	2640772
DB143046	IDH3B	1	211	20	2640212	2644850	IDH3B	208	351	20	2641517	2644136
AF023266	UBAC2	1	87	13	100038542	100038628	IDH3B	79	1357	20	2639041	2644835
U49283	UBAC2	1	87	13	100038542	100038628	IDH3B	79	1595	20	2639041	2644835

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=20)	Stat. for Synonymous SNVs (# total SNVs=6)

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
chr20:2639436-2639436	p.I373M	3
chr20:2641429-2641429	p.P149S	2
chr20:2641180-2641180	p.R196R	1
chr20:2639398-2639398	p.*386L	1
chr20:2644629-2644629	p.P20L	1
chr20:2640405-2640405	p.R317K	1
chr20:2641184-2641184	p.Q195P	1
chr20:2639399-2639399	p.*386E	1
chr20:2644651-2644651	p.A13S	1
chr20:2640407-2640407	p.G316G	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	2	2					2		3			3	3				1	3	1	4
# mutation	2	2					2		3			3	3				1	3	1	4
nonsynonymous SNV	1	2							2			1	3				1	2	1	3
synonymous SNV	1						2		1			2						1		1

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
chr20:2641562	p.L280V,IDH3B	2
chr20:2640753	p.R131W,IDH3B	2
chr20:2644817	p.R361Q	1
chr20:2639447	p.V59L,IDH3B	1
chr20:2641176	p.K350K,IDH3B	1
chr20:2639473	p.E41G,IDH3B	1
chr20:2641180	p.H335D,IDH3B	1
chr20:2640192	p.P20L,IDH3B	1
chr20:2641184	p.R317K,IDH3B	1
chr20:2640352	p.R8C,IDH3B	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 IDH3B 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 IDH3B

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


ATG101,TSR3,C20orf27,AP5S1,NDUFAF5,CENPB,DDRGK1, DTYMK,IDH3B,ITPA,MRPS26,NDUFS6,NDUFS7,NOP56, NSFL1C,PLEKHJ1,RBCK1,SNRPB,TIMM13,UBOX5,VPS16	BCKDHA,C21orf33,ECI1,EXOC3,HAX1,ICT1,IDH3B, KEAP1,MAF1,MRPL2,MRPL38,MRPS18B,MRPS5,MRPS7, NDUFB10,NDUFB9,NDUFV1,SPAG7,STK25,TACO1,WBSCR16

ANKEF1,C20orf27,AP5S1,NDUFAF5,CRLS1,CSNK2A1,DDRGK1, FASTKD5,IDH3B,ITPA,MKKS,MRPS26,NOP56,NSFL1C, PANK2,PCNA,PSMF1,SNRPB,TASP1,TRMT6,VPS16	ATP5A1,ATP5G1,CYC1,ERAL1,FBXW9,FH,IDH3B, ITPA,MDH2,MRPL12,MRPL2,MRPL38,MRPS12,NDUFS3, NDUFS6,POLDIP2,PPIA,TIMM13,UBAC1,UQCR10,UQCRC2

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 IDH3B

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00157	isocitrate dehydrogenase 3 (NAD+) beta	approved; nutraceutical	NADH

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Cross referenced IDs for IDH3B

* 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