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 ISYNA1

Basic gene info.	Gene symbol	ISYNA1
	Gene name	inositol-3-phosphate synthase 1
	Synonyms	INO1\|INOS\|IPS\|IPS 1\|IPS-1
	Cytomap	UCSC genome browser: 19p13.11
	Genomic location	chr19 :18545197-18548119
	Type of gene	protein-coding
	RefGenes	NM_001170938.1, NM_001253389.1,NM_016368.4,NR_045573.1,NR_045574.1, NM_001170939.1,
	Ensembl id	ENSG00000105655
	Description	MI-1-P synthaseMIP synthasemyo-inositol 1-phosphate synthase A1
	Modification date	20141211
dbXrefs	MIM : 611670
	HGNC : HGNC
	Ensembl : ENSG00000105655
	HPRD : 17163
	Vega : OTTHUMG00000179027
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ISYNA1
	BioGPS: 51477
	Gene Expression Atlas: ENSG00000105655
	The Human Protein Atlas: ENSG00000105655
Pathway	NCI Pathway Interaction Database: ISYNA1
	KEGG: ISYNA1
	REACTOME: ISYNA1
	ConsensusPathDB
	Pathway Commons: ISYNA1
Metabolism	MetaCyc: ISYNA1
	HUMANCyc: ISYNA1
Regulation	Ensembl's Regulation: ENSG00000105655
	miRBase: chr19 :18,545,197-18,548,119
	TargetScan: NM_001170938
	cisRED: ENSG00000105655
Context	iHOP: ISYNA1
	cancer metabolism search in PubMed: ISYNA1
	UCL Cancer Institute: ISYNA1
Assigned class in ccmGDB	C

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Phenotypic Information for ISYNA1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ISYNA1
	Familial Cancer Database: ISYNA1

* 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: ISYNA1
	MedGen: ISYNA1 (Human Medical Genetics with Condition)
	ClinVar: ISYNA1
Phenotype	MGI: ISYNA1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ISYNA1

Mutations for ISYNA1

* 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

* 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	ISYNA1	chr19	18546210	18546230	WDR87	chr19	38390134	38390154

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 ISYNA1 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
AA368753	ISYNA1	1	160	19	18547190	18547553	CSH2	158	317	17	61950608	61951036
AW962615	ISYNA1	1	159	19	18547190	18547552	CSH1	157	509	17	61973091	61973933
BF945926	ISYNA1	8	153	19	18546212	18546438	NCDN	150	229	1	36032076	36032155

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=17)	Stat. for Synonymous SNVs (# total SNVs=15)

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
chr19:18546678-18546678	p.L343L	3
chr19:18547246-18547246	p.A218V	2
chr19:18546115-18546115	p.A478V	2
chr19:18547022-18547022	p.A265A	2
chr19:18546719-18546719	p.V330M	1
chr19:18547215-18547215	p.T228T	1
chr19:18547624-18547624	p.G160E	1
chr19:18545911-18545911	p.P497S	1
chr19:18546720-18546720	p.I329I	1
chr19:18547219-18547219	p.W227*	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=1

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			6			4					3		1	1		3	4		6
# mutation	2			6			4					3		1	1		3	5		6
nonsynonymous SNV	1			4			2					2		1				2		2
synonymous SNV	1			2			2					1			1		3	3		4

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
chr19:18546722	p.L92L,ISYNA1	1
chr19:18547602	p.A350A,ISYNA1	1
chr19:18546085	p.A90V,ISYNA1	1
chr19:18546730	p.A350V,ISYNA1	1
chr19:18547641	p.S88S,ISYNA1	1
chr19:18546114	p.G344G,ISYNA1	1
chr19:18546855	p.R63C,ISYNA1	1
chr19:18547671	p.L335I,ISYNA1	1
chr19:18546115	p.P39P,ISYNA1	1
chr19:18546863	p.P259P,ISYNA1	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 ISYNA1 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 ISYNA1

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


ATG4D,C16orf13,C19orf53,CCDC124,COPE,ECI1,DDX49, E4F1,FKBP8,GPX4,ISYNA1,LSM4,NME4,NR2F6, QTRT1,RFXANK,RHPN1,SUGP1,SSBP4,UBA52,WDR83	CEP131,SYNE4,C2orf81,CACFD1,DAK,FBXW9,ISYNA1, ITGA3,LOC92659,LPAR2,LSR,MED16,NAT14,P4HTM, PAFAH1B3,PKP3,PRRG2,SYTL1,TRIM28,WDR34,XYLT2

C1QTNF8,C4orf51,CA7,CCL26,CRYBA4,GJA3,HELT, ISYNA1,KRT3,LAG3,NXPH4,TINCR,PPM1K,PRAMEF6, PRB1,PRB2,PRR4,RXFP2,TRIM69,PRSS58,WDR11	ACTBL2,CCL18,CHIT1,DEFB4A,DUOX1,FAM74A1,FAM92A1P2, FLJ25758,HS3ST2,HTRA4,ISYNA1,KRT6B,KRTAP13-1,LY6D, MMP10,PRAMEF12,RBMXL3,SLC13A4,TM4SF19,TRIM42,XKRY2

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 ISYNA1

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
DB01907	inositol-3-phosphate synthase 1	experimental	Nicotinamide-Adenine-Dinucleotide

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Cross referenced IDs for ISYNA1

* 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