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 IMPA2

Basic gene info.	Gene symbol	IMPA2
	Gene name	inositol(myo)-1(or 4)-monophosphatase 2
	Synonyms	-
	Cytomap	UCSC genome browser: 18p11.2
	Genomic location	chr18 :11981426-12030885
	Type of gene	protein-coding
	RefGenes	NM_014214.2,
	Ensembl id	ENSG00000141401
	Description	IMP 2IMPase 2inosine monophosphatase 2inositol monophosphatase 2inositol monophosphatase 2 variant 1inositol monophosphatase 2 variant 2myo-inositol monophosphatase A2
	Modification date	20141207
dbXrefs	MIM : 605922
	HGNC : HGNC
	Ensembl : ENSG00000141401
	HPRD : 09329
	Vega : OTTHUMG00000131693
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_IMPA2
	BioGPS: 3613
	Gene Expression Atlas: ENSG00000141401
	The Human Protein Atlas: ENSG00000141401
Pathway	NCI Pathway Interaction Database: IMPA2
	KEGG: IMPA2
	REACTOME: IMPA2
	ConsensusPathDB
	Pathway Commons: IMPA2
Metabolism	MetaCyc: IMPA2
	HUMANCyc: IMPA2
Regulation	Ensembl's Regulation: ENSG00000141401
	miRBase: chr18 :11,981,426-12,030,885
	TargetScan: NM_014214
	cisRED: ENSG00000141401
Context	iHOP: IMPA2
	cancer metabolism search in PubMed: IMPA2
	UCL Cancer Institute: IMPA2
Assigned class in ccmGDB	C

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Phenotypic Information for IMPA2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: IMPA2
	Familial Cancer Database: IMPA2

* 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_INOSITOL_PHOSPHATE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: IMPA2
	MedGen: IMPA2 (Human Medical Genetics with Condition)
	ClinVar: IMPA2
Phenotype	MGI: IMPA2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: IMPA2

Mutations for IMPA2

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	IMPA2	chr18	12024803	12024823		chr10	118180922	118180942

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 IMPA2 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
AA593969	LILRB4	19	111	19	55179589	55179681	IMPA2	107	411	18	12028110	12030454
BP429539	NUCB2	5	182	11	17298314	17304451	IMPA2	178	422	18	12028045	12028979

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=20)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr18:12028083-12028083	p.R178C	2
chr18:12028084-12028084	p.R178H	2
chr18:12030427-12030427	p.T279T	2
chr18:12014301-12014301	p.R140Q	2
chr18:11999115-11999115	p.L53L	1
chr18:12030410-12030410	p.A274P	1
chr18:12012174-12012174	p.P114Q	1
chr18:11999154-11999154	p.I66M	1
chr18:12030413-12030413	p.Q275*	1
chr18:12012195-12012195	p.G121V	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=5

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	1			4			2		3			1		1			4	2		5
# mutation	1			4			2		3			1		1			4	2		6
nonsynonymous SNV	1			3			1		2			1		1			1	1		5
synonymous SNV				1			1		1								3	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
chr18:12028083	p.R178C	2
chr18:12028084	p.R178H	2
chr18:12030427	p.T279T	2
chr18:12012207	p.F122S	1
chr18:12030440	p.R125Q	1
chr18:12014301	p.R140Q	1
chr18:11999053	p.K167K	1
chr18:12028052	p.R178R	1
chr18:11999101	p.P180H	1
chr18:11999109	p.I33V	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 IMPA2 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 IMPA2

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


AFG3L2,ART3,ATAD3A,AURKB,C9orf40,CDC20,CDCA8, ECE2,EN1,FANCE,HMGA1,IMPA2,NCS1,NDC80, RBM17,RRP1,SEH1L,STMN1,THEM5,TYMS,ZDHHC18	AK1,AKR1B1,ALDOA,BIN1,COX7A1,YBX3,CUTC, IL17D,IMPA2,KCNJ12,LINC00116,PAQR9,PINK1,PPAPDC3, RAD23A,SCN1B,SHISA4,SIRT2,TPI1,UBAC1,VDAC3

AFG3L2,ASRGL1,ATOH1,CAPN9,CHST5,FAM174B,GALNTL6, FFAR4,IMPA2,KIAA1324,KLF4,KLK1,PTGER2,SEH1L, SGSM3,SIDT1,SPINK4,ST6GALNAC1,TOX,TYMS,XBP1	ADCK2,APH1A,CANT1,CDX1,COG2,ERGIC3,FXYD3, IMPA2,LRRC31,LRRC57,MAN1B1,PCTP,PLBD1,PPP1R1B, PXMP2,QARS,RAB25,SMAGP,SMPDL3B,TEX264,TRAPPC6A

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 IMPA2

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
DB01356	inositol(myo)-1(or 4)-monophosphatase 2	approved	Lithium

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Cross referenced IDs for IMPA2

* 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