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 INPP4B

Basic gene info.	Gene symbol	INPP4B
	Gene name	inositol polyphosphate-4-phosphatase, type II, 105kDa
	Synonyms	-
	Cytomap	UCSC genome browser: 4q31.21
	Genomic location	chr4 :142949181-143767604
	Type of gene	protein-coding
	RefGenes	NM_001101669.1, NM_003866.2,
	Ensembl id	ENSG00000109452
	Description	inositol polyphosphate 4-phosphatase II; 4-phosphatase IIinositol polyphosphate 4-phosphatase type IIinositol polyphosphate-4-phosphatase, type II, 105kDtype II inositol 3,4-bisphosphate 4-phosphatasetype II inositol-3,4-bisphosphate 4-phosphatase
	Modification date	20141207
dbXrefs	MIM : 607494
	HGNC : HGNC
	Ensembl : ENSG00000109452
	HPRD : 06322
	Vega : OTTHUMG00000161341
Protein	UniProt: O15327 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_INPP4B
	BioGPS: 8821
	Gene Expression Atlas: ENSG00000109452
	The Human Protein Atlas: ENSG00000109452
Pathway	NCI Pathway Interaction Database: INPP4B
	KEGG: INPP4B
	REACTOME: INPP4B
	ConsensusPathDB
	Pathway Commons: INPP4B
Metabolism	MetaCyc: INPP4B
	HUMANCyc: INPP4B
Regulation	Ensembl's Regulation: ENSG00000109452
	miRBase: chr4 :142,949,181-143,767,604
	TargetScan: NM_001101669
	cisRED: ENSG00000109452
Context	iHOP: INPP4B
	cancer metabolism search in PubMed: INPP4B
	UCL Cancer Institute: INPP4B
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of INPP4B in cancer cell metabolism	1. Min JW, Kim KI, Kim HA, Kim EK, Noh WC, et al. (2013) INPP4B-mediated tumor resistance is associated with modulation of glucose metabolism via hexokinase 2 regulation in laryngeal cancer cells. Biochem Biophys Res Commun 440: 137-142. doi: 10.1016/j.bbrc.2013.09.041. go to article 2. Lopez SM, Hodgson MC, Packianathan C, Bingol-Ozakpinar O, Uras F, et al. (2013) Determinants of the tumor suppressor INPP4B protein and lipid phosphatase activities. Biochem Biophys Res Commun 440: 277-282. doi: 10.1016/j.bbrc.2013.09.077. go to article 3. Zhang X, Chen H, Wang X, Zhao W, Chen JJ (2014) Expression and transcriptional profiling of the LKB1 tumor suppressor in cervical cancer cells. Gynecol Oncol 134: 372-378. doi: 10.1016/j.ygyno.2014.04.050. go to article

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Phenotypic Information for INPP4B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: INPP4B
	Familial Cancer Database: INPP4B

* 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 REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	607494; gene.
Orphanet
Disease	KEGG Disease: INPP4B
	MedGen: INPP4B (Human Medical Genetics with Condition)
	ClinVar: INPP4B
Phenotype	MGI: INPP4B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: INPP4B

Mutations for INPP4B

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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	INPP4B	chr4	142966858	142966878		chr4	142708424	142708444
ovary	INPP4B	chr4	143112579	143112599		chr8	42120902	42120922
ovary	INPP4B	chr4	143112771	143112791	SLC20A2	chr8	42289672	42289692
ovary	INPP4B	chr4	143162513	143162533	INPP4B	chr4	143158755	143158775
ovary	INPP4B	chr4	143353923	143353943		chr4	144708014	144708034
ovary	INPP4B	chr4	143376718	143376738	INPP4B	chr4	143373158	143373178
ovary	INPP4B	chr4	143502810	143502830	DEPTOR	chr8	121037892	121037912
pancreas	INPP4B	chr4	142971601	142971621	INPP4B	chr4	142971722	142971742
pancreas	INPP4B	chr4	142975114	142975134	INPP4B	chr4	142975210	142975230
pancreas	INPP4B	chr4	143018635	143018655		chr4	155616362	155616382
pancreas	INPP4B	chr4	143044679	143044699	INPP4B	chr4	143046841	143046861
pancreas	INPP4B	chr4	143130541	143130561	INPP4B	chr4	143617879	143617899
pancreas	INPP4B	chr4	143598663	143598683	INPP4B	chr4	143578418	143578438
pancreas	INPP4B	chr4	143756618	143756638	GAB1	chr4	144393092	144393112

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 INPP4B 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
DB020243	INPP4B	1	239	4	143687891	143689122	IST1	237	544	16	71924472	71928762
BP360877	MAPK10	1	511	4	87275682	87281206	INPP4B	510	582	4	143067074	143067145
AK057258	INPP4B	1	238	4	143687891	143689122	IST1	236	1735	16	71924472	71961793
CB044109	INPP4B	189	243	4	142963302	142963356	GPX3	242	672	5	150406475	150407696
BG990026	INPP4B	17	36	4	142957046	142957065	ELL3	30	318	15	44084546	44086052
S60878	INPP4B	8	34	4	143719085	143719135	WBSCR17	15	35	7	70897786	70897806
BF895764	SKAP2	31	441	7	26813062	26813470	INPP4B	436	488	4	143233000	143233052
BG952183	EGFLAM	119	156	5	38320667	38320731	INPP4B	143	311	4	143072468	143072636

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	3	1		1			5		2		3			2	2		4
GAIN (# sample)	2			1			3		2		2			1	1		2
LOSS (# sample)	1	1					2				1			1	1		2

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=111)	Stat. for Synonymous SNVs (# total SNVs=29)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=3)

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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
chr4:143081713-143081713	p.T454R	4
chr4:143159105-143159105	p.R250*	4
chr4:143324153-143324153	p.I104V	4
chr4:143094806-143094806	p.S446S	3
chr4:143067097-143067097	p.V539A	3
chr4:143029297-143029297	p.E775K	3
chr4:143130163-143130163	p.E285*	2
chr4:143007359-143007359	p.L809I	2
chr4:143159104-143159104	p.R250Q	2
chr4:143094812-143094812	p.K444N	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	5	6		13			6		2	1		20	4	2			3	8		15
# mutation	5	6		15			7		2	1		21	5	2			3	9		17
nonsynonymous SNV	3	5		11			6		1	1		14	5	2			2	6		11
synonymous SNV	2	1		4			1		1			7					1	3		6

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
chr4:143029297	p.E775K,INPP4B	3
chr4:143181690	p.L809I,INPP4B	2
chr4:143007359	p.P215T,INPP4B	2
chr4:143181714	p.A207S,INPP4B	2
chr4:143159104	p.R250Q,INPP4B	2
chr4:143114276	p.G660G,INPP4B	1
chr4:143324110	p.L447F,INPP4B	1
chr4:143029298	p.W248S,INPP4B	1
chr4:143044560	p.G146G,INPP4B	1
chr4:143159161	p.G7V,INPP4B	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 INPP4B 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 INPP4B

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.

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Protein Expression Plot (RPPA)

*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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


AFF1,AHNAK,ARFIP1,ATG2B,BOD1L1,SMIM14,CREBRF, CCNG2,FNIP1,INPP4B,KIAA0232,KIAA1109,LCOR,LRBA, MAP3K1,MKL2,PTPN13,RAB27B,STAM2,WDFY3,ZNF844	AFF3,ANKRD30A,ANKS1B,ARHGAP32,ERBB4,FAM161B,IGF1R, INPP4B,IQCH,LYPD6,MAGI3,MYB,MYO6,JADE3, RAB27B,RABEP1,RASEF,ST8SIA6,SYTL2,SYTL5,TSPAN5

ACTBL2,ANXA8,BPI,C8orf86,CGB1,CPA4,CST6, FAM3C,IL20RB,INPP4B,LIPK,LRAT,MUC16,MYH16, PEX5L,PSG6,PSG9,SIGLEC15,THEG,WNT7A,ZNF365	CAST,CEBPG,CORO2A,DHCR24,GPD2,INPP4B,KIF16B, LHFPL2,LUZP1,PICALM,PLS1,PSMD11,RAB14,RNF103, SLC41A2,SMAP1,TMEM135,TOP1P1,UGCG,VDAC1,ZDHHC21

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 INPP4B

There's no related Drug.

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Cross referenced IDs for INPP4B

* 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