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 INPPL1

Basic gene info.	Gene symbol	INPPL1
	Gene name	inositol polyphosphate phosphatase-like 1
	Synonyms	OPSMD\|SHIP2
	Cytomap	UCSC genome browser: 11q13
	Genomic location	chr11 :71935881-71950188
	Type of gene	protein-coding
	RefGenes	NM_001567.3,
	Ensembl id	ENSG00000165458
	Description	51C proteinINPPL-1SH2 domain-containing inositol 5'-phosphatase 2SH2 domain-containing inositol-5'-phosphatase 2SHIP-2phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2protein 51C
	Modification date	20141207
dbXrefs	MIM : 600829
	HGNC : HGNC
	Ensembl : ENSG00000165458
	HPRD : 02900
	Vega : OTTHUMG00000167879
Protein	UniProt: O15357 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_INPPL1
	BioGPS: 3636
	Gene Expression Atlas: ENSG00000165458
	The Human Protein Atlas: ENSG00000165458
Pathway	NCI Pathway Interaction Database: INPPL1
	KEGG: INPPL1
	REACTOME: INPPL1
	ConsensusPathDB
	Pathway Commons: INPPL1
Metabolism	MetaCyc: INPPL1
	HUMANCyc: INPPL1
Regulation	Ensembl's Regulation: ENSG00000165458
	miRBase: chr11 :71,935,881-71,950,188
	TargetScan: NM_001567
	cisRED: ENSG00000165458
Context	iHOP: INPPL1
	cancer metabolism search in PubMed: INPPL1
	UCL Cancer Institute: INPPL1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for INPPL1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: INPPL1
	Familial Cancer Database: INPPL1

* 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 UCEC ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
7Therapeutic 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	125853; phenotype. 258480; phenotype. 600829; gene.
Orphanet	2746; Opsismodysplasia.
Disease	KEGG Disease: INPPL1
	MedGen: INPPL1 (Human Medical Genetics with Condition)
	ClinVar: INPPL1
Phenotype	MGI: INPPL1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: INPPL1

Mutations for INPPL1

* 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 INPPL1 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
BE280713	INPPL1	1	444	11	71944488	71946231	INPPL1	436	460	11	71946224	71946248
BE765401	INPPL1	17	139	11	71944142	71944542	INPPL1	133	262	11	71944753	71945418
BC071891	INPPL1	22	307	11	71948741	71949358	NPM1	308	1586	5	170814870	170837881
BG991798	INPPL1	19	391	11	71949304	71949677	INPPL1	385	491	11	71946193	71946391
BF990573	INPPL1	1	93	11	71940704	71940796	COIL	83	165	17	55016435	55016517

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=84)	Stat. for Synonymous SNVs (# total SNVs=32)

Stat. for Deletions (# total SNVs=5)	Stat. for Insertions (# total SNVs=2)

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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
chr11:71946427-71946427	p.G864D	4
chr11:71948748-71948748	p.R1156fs*46	3
chr11:71942192-71942192	p.R486C	3
chr11:71949087-71949087	p.A1185D	3
chr11:71940223-71940223	p.H203P	2
chr11:71943960-71943960	p.L631L	2
chr11:71946494-71946494	p.Y886Y	2
chr11:71943961-71943961	p.L632I	2
chr11:71941449-71941449	p.G378G	2
chr11:71946908-71946908	p.P919P	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=4

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	4	6		19	1		2		1	1		12	2	3			13	12	1	16
# mutation	5	6		15	1		1		1	1		13	2	3			17	12	1	22
nonsynonymous SNV	3	4		9	1		1		1	1		9	2	1			9	10		14
synonymous SNV	2	2		6								4		2			8	2	1	8

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
chr11:71939260	p.R70H	3
chr11:71942192	p.R486C	3
chr11:71946427	p.G864D	3
chr11:71942228	p.G378G	2
chr11:71946494	p.Y886Y	2
chr11:71941250	p.A1185D	2
chr11:71941449	p.P143P	2
chr11:71939802	p.R342Q	2
chr11:71942214	p.T493M	2
chr11:71949087	p.R498S	2

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 INPPL1 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 INPPL1

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


ARAP1,ARHGEF17,ARRB1,ATG16L2,ANAPC15,LAMTOR1,CLPB, ELMO3,INPPL1,KIAA0895L,LRTOMT,NUMA1,PCNXL3,PHRF1, RELT,RNF121,RTEL1,TNRC18,ULK1,ZFYVE27,ZNF512B	ATG4D,ATXN7L2,BAG6,D2HGDH,DPP9,DVL1,GTF3C1, INPPL1,INTS1,MARK4,MIB2,MYO18A,PANK4,PTCD1, PPP6R2,SPG7,TARS2,TMEM201,UCKL1,USP19,ZNF76

ANKRD13D,ARAP1,CEP164,CEP250,CRAMP1L,DENND4B,DOCK6, LINC01000,GIGYF1,IGHMBP2,INPPL1,KDM2A,NFRKB,NUMA1, PCNXL3,SETD1A,SIN3B,SLC26A1,SRRM2,ZNF142,ZNF335	ANKRD11,PRRC2A,SLX4,HECTD4,CAMTA2,CIC,CRAMP1L, FAM160B2,FAM193A,GIGYF1,GYS1,INPPL1,GSE1,PSMG3-AS1, NEURL4,PLCG1,PLXNB1,PRR12,SETD1B,SH3PXD2A,SIN3B

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 INPPL1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	O15357; -.
Chemistry	ChEMBL	CHEMBL2331064; -.
Organism-specific databases	PharmGKB	PA29888; -.
Organism-specific databases	CTD	3636; -.

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
DB00877	inositol polyphosphate phosphatase-like 1	approved; investigational	Sirolimus

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Cross referenced IDs for INPPL1

* 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