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 IMPDH2

Basic gene info.	Gene symbol	IMPDH2
	Gene name	IMP (inosine 5'-monophosphate) dehydrogenase 2
	Synonyms	IMPD2\|IMPDH-II
	Cytomap	UCSC genome browser: 3p21.2
	Genomic location	chr3 :49061761-49066875
	Type of gene	protein-coding
	RefGenes	NM_000884.2,
	Ensembl id	ENSG00000178035
	Description	IMP (inosine monophosphate) dehydrogenase 2IMP oxireductase 2IMPD 2IMPDH 2inosine 5' phosphate dehydrogenase 2inosine monophosphate dehydrogenase type IIinosine-5'-monophosphate dehydrogenase 2
	Modification date	20141207
dbXrefs	MIM : 146691
	HGNC : HGNC
	Ensembl : ENSG00000178035
	HPRD : 00895
	Vega : OTTHUMG00000156771
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_IMPDH2
	BioGPS: 3615
	Gene Expression Atlas: ENSG00000178035
	The Human Protein Atlas: ENSG00000178035
Pathway	NCI Pathway Interaction Database: IMPDH2
	KEGG: IMPDH2
	REACTOME: IMPDH2
	ConsensusPathDB
	Pathway Commons: IMPDH2
Metabolism	MetaCyc: IMPDH2
	HUMANCyc: IMPDH2
Regulation	Ensembl's Regulation: ENSG00000178035
	miRBase: chr3 :49,061,761-49,066,875
	TargetScan: NM_000884
	cisRED: ENSG00000178035
Context	iHOP: IMPDH2
	cancer metabolism search in PubMed: IMPDH2
	UCL Cancer Institute: IMPDH2
Assigned class in ccmGDB	C

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Phenotypic Information for IMPDH2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: IMPDH2
	Familial Cancer Database: IMPDH2

* 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
KEGG_PURINE_METABOLISM KEGG_DRUG_METABOLISM_OTHER_ENZYMES REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: IMPDH2
	MedGen: IMPDH2 (Human Medical Genetics with Condition)
	ClinVar: IMPDH2
Phenotype	MGI: IMPDH2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: IMPDH2

Mutations for IMPDH2

* 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 IMPDH2 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

BU675368

IMPDH2

123

49061758

49061967

IMPDH2

109

484

49061814

49062452

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=35)	Stat. for Synonymous SNVs (# total SNVs=18)

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
chr3:49065296-49065296	p.R126R	3
chr3:49065703-49065703	p.A101V	2
chr3:49064262-49064262	p.D226G	2
chr3:49063960-49063960	p.G301A	2
chr3:49062587-49062587	p.A374A	2
chr3:49064436-49064436	p.I192I	1
chr3:49062338-49062338	p.R429K	1
chr3:49062644-49062644	p.R355R	1
chr3:49065295-49065295	p.V127M	1
chr3:49064190-49064190	p.I250S	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		10	2		1		2			2	1	1			3	4	2	6
# mutation	3	2		10	2		1		2			2	1	1			3	4	2	8
nonsynonymous SNV	2	1		6					2			2	1				1	2	2	3
synonymous SNV	1	1		4	2		1							1			2	2		5

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
chr3:49064262	p.D226G	2
chr3:49066721	p.R161K	1
chr3:49062388	p.R355R	1
chr3:49064248	p.S159F	1
chr3:49065256	p.R355W	1
chr3:49066745	p.I330T	1
chr3:49062461	p.C140C	1
chr3:49065295	p.R322Q	1
chr3:49062587	p.C140S	1
chr3:49064276	p.N303I	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 IMPDH2 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 IMPDH2

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


ACY1,DALRD3,GNB2L1,IMPDH2,QARS,RPL10A,RPL13A, RPL14,RPL15,RPL26,RPL29,RPL3,RPL41,RPL7A, RPLP0,RPS14,RPS23,RPS5,RPSA,RPSAP58,SNHG8	ALKBH2,C19orf48,EEF1G,EIF3D,FBL,GNB2L1,IMPDH2, NOB1,RPL10A,RPL12,RPL13A,RPL3,RPL7A,RPLP0, RPS18,RPS19,RPS2,RPS3,RPS5,RPS8,RPSAP58

C19orf48,EEF1A1P9,EEF1G,EEF2,EIF3D,EIF3L,HNRNPA1L2, IMPDH2,NDUFV1,NLE1,POLL,QARS,RPL12,RPL13A, RPL29,RPL3,RPLP0,RPS2,RPS29,RPSAP58,TKT	C19orf48,CHTF8,EEF1G,EIF3D,EXOSC5,FBL,GNB2L1, HNRNPA1L2,IMPDH2,KDM1A,NARS2,NLE1,NOB1,NONO, PTDSS1,RPL23A,RPL3,RPS12,RPS2,THG1L,TRAP1

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 IMPDH2

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	IMP (inosine 5'-monophosphate) dehydrogenase 2	approved; nutraceutical	NADH
DB00688	IMP (inosine 5'-monophosphate) dehydrogenase 2	approved; investigational	Mycophenolate mofetil
DB01024	IMP (inosine 5'-monophosphate) dehydrogenase 2	approved	Mycophenolic acid
DB01693	IMP (inosine 5'-monophosphate) dehydrogenase 2	experimental	Ribavirin Monophosphate
DB01907	IMP (inosine 5'-monophosphate) dehydrogenase 2	experimental	Nicotinamide-Adenine-Dinucleotide
DB03070	IMP (inosine 5'-monophosphate) dehydrogenase 2	experimental	Selenazole-4-Carboxyamide-Adenine Dinucleotide
DB03948	IMP (inosine 5'-monophosphate) dehydrogenase 2	experimental	6-Chloropurine Riboside, 5'-Monophosphate
DB04566	IMP (inosine 5'-monophosphate) dehydrogenase 2	experimental	Inosinic Acid
DB00993	IMP (inosine 5'-monophosphate) dehydrogenase 2	approved	Azathioprine
DB00158	IMP (inosine 5'-monophosphate) dehydrogenase 2	approved; nutraceutical	Folic Acid
DB00563	IMP (inosine 5'-monophosphate) dehydrogenase 2	approved	Methotrexate

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Cross referenced IDs for IMPDH2

* 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