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 GPHN
Basic gene info.Gene symbolGPHN
Gene namegephyrin
SynonymsGEPH|GPH|GPHRYN|HKPX1|MOCODC
CytomapUCSC genome browser: 14q23.3
Genomic locationchr14 :66974124-67648525
Type of geneprotein-coding
RefGenesNM_001024218.1,
NM_020806.4,
Ensembl idENSG00000171723
Description-
Modification date20141219
dbXrefs MIM : 603930
HGNC : HGNC
Ensembl : ENSG00000171723
HPRD : 04893
Vega : OTTHUMG00000029785
ProteinUniProt: Q9NQX3
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPHN
BioGPS: 10243
Gene Expression Atlas: ENSG00000171723
The Human Protein Atlas: ENSG00000171723
PathwayNCI Pathway Interaction Database: GPHN
KEGG: GPHN
REACTOME: GPHN
ConsensusPathDB
Pathway Commons: GPHN
MetabolismMetaCyc: GPHN
HUMANCyc: GPHN
RegulationEnsembl's Regulation: ENSG00000171723
miRBase: chr14 :66,974,124-67,648,525
TargetScan: NM_001024218
cisRED: ENSG00000171723
ContextiHOP: GPHN
cancer metabolism search in PubMed: GPHN
UCL Cancer Institute: GPHN
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GPHN(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPHN
Familial Cancer Database: GPHN
* 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
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

check002.gifOthers
OMIM 603930; gene.
615501; phenotype.
Orphanet 308400; Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C.
3197; Hereditary hyperekplexia.
DiseaseKEGG Disease: GPHN
MedGen: GPHN (Human Medical Genetics with Condition)
ClinVar: GPHN
PhenotypeMGI: GPHN (International Mouse Phenotyping Consortium)
PhenomicDB: GPHN

Mutations for GPHN
* 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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryGPHNchr146728399867284018GPHNchr146728419967284219
ovaryGPHNchr146748216867482188GPHNchr146748249967482519
pancreasGPHNchr146708799267088192GPHNchr146708370867083908
pancreasGPHNchr146758867467588694GPHNchr146762311667623136
pancreasGPHNchr146762069367620713GPHNchr146761053367610553
prostateGPHNchr146699056266992562RGS6chr147264472372646723
prostateGPHNchr146699088266992882RGS6chr147280878772810787
prostateGPHNchr146716191467163914DPF3chr147334995573351955
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 GPHN related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB087988USP6NL1225101163962911653573GPHN225462146729119267382765
BX509307GPHN188146710248467102571CCDC128365834698222846982802
BE172739DNM1L23143123289683332896951GPHN125245146762545767625577

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 # sample521   1   1  12  
GAIN (# sample)11            1  
LOSS (# sample)411   1   1  11  
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=11)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr14:67578599-67578599p.R479*2
chr14:67346679-67346679p.R106Q1
chr14:67389434-67389434p.R170C1
chr14:67389594-67389594p.G223A1
chr14:67525489-67525489p.I377N1
chr14:67589031-67589031p.T562S1
chr14:67626169-67626169p.A625V1
chr14:67631930-67631930p.I654M1
chr14:67635728-67635728p.P685L1
chr14:67147816-67147816p.?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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13 15  1 41 312  98 11
# mutation13 14  1 41 312  1110 20
nonsynonymous SNV12 12  1 31 3 2  810 16
synonymous SNV 1 2    1   1   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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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
chr14:67589024p.A592V,GPHN3
chr14:67626169p.R527C,GPHN3
chr14:67567593p.I344I,GPHN2
chr14:67525490p.R387C,GPHN2
chr14:67631930p.I621M,GPHN2
chr14:67389441p.Y673C,GPHN1
chr14:67589003p.E4K,GPHN1
chr14:67431951p.E213G,GPHN1
chr14:67635650p.I344N,GPHN1
chr14:67647611p.T541T,GPHN1

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 GPHN 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 GPHN

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

ATP6V1C1,DHRS4-AS1,LINC00238,C8orf37,DNAL1,EARS2,EBAG9,
EXD2,FLNB,GPHN,MAPT,MBLAC2,OCIAD1,PARD6B,
RAD17,SLC39A9,STAU2,TMEM128,TRPS1,UBXN2B,WWP1
ABCB7,AGPAT9,ALDH1L1,AMBN,BMP3,C17orf53,IZUMO4,
CTH,EYA1,GLUL,GMCL1,GPD1L,GPHN,HADH,
MOCS1,NTSR2,PMM1,PXMP2,RASL10B,TCEB3,USP30

ALDH6A1,LINC00238,CDKL1,DHRS4L2,DLST,EPHB3,GPHN,
IMPDH2,KIAA0586,L2HGDH,LRP4,MMACHC,MTHFD1,AP5M1,
OXA1L,RGMB,SAMM50,SETD3,SIPA1L1,TRMT5,WDR89
ANAPC1,AQR,ATIC,PROSER1,CBX5,CCDC15,DCAF7,
EXOSC10,GANAB,GPHN,INCENP,INTS9,FOCAD,NCAPD2,
PAXIP1,PTK7,SND1,SPTLC2,SSRP1,TOP2A,VPRBP
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 GPHN
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28840; -.
Organism-specific databasesCTD 10243; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01942gephyrinexperimentalFormic Acid
DB03766gephyrinexperimentalPropanoic Acid


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Cross referenced IDs for GPHN
* 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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