Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 SYNJ1
Basic gene info.Gene symbolSYNJ1
Gene namesynaptojanin 1
SynonymsINPP5G|PARK20
CytomapUCSC genome browser: 21q22.2
Genomic locationchr21 :34001068-34100351
Type of geneprotein-coding
RefGenesNM_001160302.1,
NM_001160306.1,NM_003895.3,NM_203446.2,
Ensembl idENSG00000159082
Descriptioninositol 5'-phosphatase (synaptojanin 1)synaptic inositol 1,4,5-trisphosphate 5-phosphatase 1synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1synaptojanin-1synaptojanin-1, polyphosphoinositide phosphatase
Modification date20141207
dbXrefs MIM : 604297
HGNC : HGNC
Ensembl : ENSG00000159082
HPRD : 09182
Vega : OTTHUMG00000064926
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SYNJ1
BioGPS: 8867
Gene Expression Atlas: ENSG00000159082
The Human Protein Atlas: ENSG00000159082
PathwayNCI Pathway Interaction Database: SYNJ1
KEGG: SYNJ1
REACTOME: SYNJ1
ConsensusPathDB
Pathway Commons: SYNJ1
MetabolismMetaCyc: SYNJ1
HUMANCyc: SYNJ1
RegulationEnsembl's Regulation: ENSG00000159082
miRBase: chr21 :34,001,068-34,100,351
TargetScan: NM_001160302
cisRED: ENSG00000159082
ContextiHOP: SYNJ1
cancer metabolism search in PubMed: SYNJ1
UCL Cancer Institute: SYNJ1
Assigned class in ccmGDBC

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Phenotypic Information for SYNJ1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SYNJ1
Familial Cancer Database: SYNJ1
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SYNJ1
MedGen: SYNJ1 (Human Medical Genetics with Condition)
ClinVar: SYNJ1
PhenotypeMGI: SYNJ1 (International Mouse Phenotyping Consortium)
PhenomicDB: SYNJ1

Mutations for SYNJ1
* 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
breastSYNJ1chr213404562234045622SYNJ1chr213408179234081792
pancreasSYNJ1chr213405229334052313chr213452251634522536
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 SYNJ1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP366199SYNJ11486213401874434029070SYNJ1482582213409916734100186

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample11               
GAIN (# sample)11               
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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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=10

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=115)
Stat. for Synonymous SNVs
(# total SNVs=36)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=4)

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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
chr21:34011221-34011221p.P1304P6
chr21:34045731-34045731p.R549C5
chr21:34011222-34011222p.P1304Q4
chr21:34003930-34003930p.V1366A3
chr21:34045776-34045776p.R534*3
chr21:34038258-34038258p.P714S3
chr21:34003928-34003929p.V1366_L1367insNT3
chr21:34012016-34012016p.P1221L2
chr21:34059352-34059352p.K295R2
chr21:34014274-34014274p.R1174C2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22126  8 5 11088 1228 23
# mutation22125  9 5 11088 1269 33
nonsynonymous SNV21116  6 3 1856 1216 29
synonymous SNV 1 9  3 2  232  53 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
chr21:34045731p.R544C,SYNJ15
chr21:34011222p.P1257Q,SYNJ14
chr21:34012087p.K343N,SYNJ12
chr21:34099161p.R704Q,SYNJ12
chr21:34058111p.V857V,SYNJ12
chr21:34029206p.S430S,SYNJ12
chr21:34004044p.S86Y,SYNJ12
chr21:34058147p.D72H,SYNJ12
chr21:34053869p.L1281P,SYNJ12
chr21:34072370p.T1150T,SYNJ12

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 SYNJ1 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 SYNJ1

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

APC,ASXL2,BIRC6,ERCC6L2,GPATCH11,CCNT1,CEP97,
DNAJB14,HCFC2,HEATR5B,IFNAR1,MORC3,PIKFYVE,PREPL,
RNF111,LTN1,SLC25A40,SON,SYNJ1,TTBK2,ZBTB11
ACAP2,BMPR2,CAMSAP2,CSGALNACT2,DNAJC13,DOCK4,EEA1,
ELK4,FRYL,HCFC2,HIPK1,ITSN2,KIAA1033,LYST,
MTMR9,PIK3C2A,POLK,SETX,SYNJ1,VPS13C,WDR44

AKAP13,CCDC88A,DOCK10,FAM63B,FLI1,HERC1,HIPK3,
IFNAR2,IL6ST,ITGA4,MORC3,MYO5A,MYO9A,PLXNC1,
PEAK1,SLC12A6,SON,SYNJ1,TAOK1,TTBK2,ZNF366
AHCTF1,ATG2B,CDC42BPA,CHD8,DYNC1H1,DYRK1A,GLG1,
GOLGB1,IRGQ,KDM2A,KIAA2026,LRP1,NIPBL,PIK3R4,
SON,SOS1,SPEN,SYNJ1,TNRC6B,UBN2,VPS13D
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 SYNJ1


There's no related Drug.
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Cross referenced IDs for SYNJ1
* 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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