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 symbolISYNA1
Gene nameinositol-3-phosphate synthase 1
SynonymsINO1|INOS|IPS|IPS 1|IPS-1
CytomapUCSC genome browser: 19p13.11
Genomic locationchr19 :18545197-18548119
Type of geneprotein-coding
RefGenesNM_001170938.1,
NM_001253389.1,NM_016368.4,NR_045573.1,NR_045574.1,
NM_001170939.1,
Ensembl idENSG00000105655
DescriptionMI-1-P synthaseMIP synthasemyo-inositol 1-phosphate synthase A1
Modification date20141211
dbXrefs MIM : 611670
HGNC : HGNC
Ensembl : ENSG00000105655
HPRD : 17163
Vega : OTTHUMG00000179027
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ISYNA1
BioGPS: 51477
Gene Expression Atlas: ENSG00000105655
The Human Protein Atlas: ENSG00000105655
PathwayNCI Pathway Interaction Database: ISYNA1
KEGG: ISYNA1
REACTOME: ISYNA1
ConsensusPathDB
Pathway Commons: ISYNA1
MetabolismMetaCyc: ISYNA1
HUMANCyc: ISYNA1
RegulationEnsembl's Regulation: ENSG00000105655
miRBase: chr19 :18,545,197-18,548,119
TargetScan: NM_001170938
cisRED: ENSG00000105655
ContextiHOP: ISYNA1
cancer metabolism search in PubMed: ISYNA1
UCL Cancer Institute: ISYNA1
Assigned class in ccmGDBC

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Phenotypic Information for ISYNA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ISYNA1
MedGen: ISYNA1 (Human Medical Genetics with Condition)
ClinVar: ISYNA1
PhenotypeMGI: ISYNA1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryISYNA1chr191854621018546230WDR87chr193839013438390154
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ISYNA1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA368753ISYNA11160191854719018547553CSH2158317176195060861951036
AW962615ISYNA11159191854719018547552CSH1157509176197309161973933
BF945926ISYNA18153191854621218546438NCDN15022913603207636032155

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr19:18546678-18546678p.L343L3
chr19:18547246-18547246p.A218V2
chr19:18546115-18546115p.A478V2
chr19:18547022-18547022p.A265A2
chr19:18546719-18546719p.V330M1
chr19:18547215-18547215p.T228T1
chr19:18547624-18547624p.G160E1
chr19:18545911-18545911p.P497S1
chr19:18546720-18546720p.I329I1
chr19:18547219-18547219p.W227*1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample2  6  4    3 11 34 6
# mutation2  6  4    3 11 35 6
nonsynonymous SNV1  4  2    2 1   2 2
synonymous SNV1  2  2    1  1 33 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr19:18546722p.L92L,ISYNA11
chr19:18547602p.A350A,ISYNA11
chr19:18546085p.A90V,ISYNA11
chr19:18546730p.A350V,ISYNA11
chr19:18547641p.S88S,ISYNA11
chr19:18546114p.G344G,ISYNA11
chr19:18546855p.R63C,ISYNA11
chr19:18547671p.L335I,ISYNA11
chr19:18546115p.P39P,ISYNA11
chr19:18546863p.P259P,ISYNA11

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01907inositol-3-phosphate synthase 1experimentalNicotinamide-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



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