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 GUCY2D
Basic gene info.Gene symbolGUCY2D
Gene nameguanylate cyclase 2D, membrane (retina-specific)
SynonymsCORD5|CORD6|CYGD|GUC1A4|GUC2D|LCA|LCA1|RCD2|RETGC-1|ROS-GC1|ROSGC|retGC
CytomapUCSC genome browser: 17p13.1
Genomic locationchr17 :7905987-7923658
Type of geneprotein-coding
RefGenesNM_000180.3,
Ensembl idENSG00000132518
DescriptionROS-GCcone rod dystrophy 6guanylate cyclase 2D, retinalretinal guanylate cyclase 1retinal guanylyl cyclase 1rod outer segment membrane guanylate cyclase
Modification date20141221
dbXrefs MIM : 600179
HGNC : HGNC
Ensembl : ENSG00000132518
HPRD : 02550
Vega : OTTHUMG00000108169
ProteinUniProt: Q02846
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GUCY2D
BioGPS: 3000
Gene Expression Atlas: ENSG00000132518
The Human Protein Atlas: ENSG00000132518
PathwayNCI Pathway Interaction Database: GUCY2D
KEGG: GUCY2D
REACTOME: GUCY2D
ConsensusPathDB
Pathway Commons: GUCY2D
MetabolismMetaCyc: GUCY2D
HUMANCyc: GUCY2D
RegulationEnsembl's Regulation: ENSG00000132518
miRBase: chr17 :7,905,987-7,923,658
TargetScan: NM_000180
cisRED: ENSG00000132518
ContextiHOP: GUCY2D
cancer metabolism search in PubMed: GUCY2D
UCL Cancer Institute: GUCY2D
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GUCY2D(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GUCY2D
Familial Cancer Database: GUCY2D
* 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_PURINE_METABOLISM

check002.gifOthers
OMIM 204000; phenotype.
600179; gene.
601777; phenotype.
Orphanet 1872; Cone rod dystrophy.
65; Leber congenital amaurosis.
75377; Central areolar choroidal dystrophy.
DiseaseKEGG Disease: GUCY2D
MedGen: GUCY2D (Human Medical Genetics with Condition)
ClinVar: GUCY2D
PhenotypeMGI: GUCY2D (International Mouse Phenotyping Consortium)
PhenomicDB: GUCY2D

Mutations for GUCY2D
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GUCY2D related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample          1      
GAIN (# sample)          1      
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=0)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no ns-snv.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

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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
# sample33 131 5 21153   1711 7
# mutation33 141 6 21153   1814 10
nonsynonymous SNV22 121 4 11132   913 7
synonymous SNV11 3  2 1  21   91 3
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
chr17:7918754p.R383R2
chr17:7907263p.E265K2
chr17:7909801p.V960M2
chr17:7917215p.S272F2
chr17:7907241p.R761W2
chr17:7909741p.K806N1
chr17:7915820p.R208R1
chr17:7910008p.G348S1
chr17:7917239p.V487M1
chr17:7907256p.G661G1

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 GUCY2D 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 GUCY2D

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

ALOX15B,ARRDC1,TMEM256,DCXR,DERL3,EPB42,GALM,
GUCY2D,HAAO,LENG1,LENG9,MMAB,MRPL41,MRPL53,
MVK,NDUFA3,PATE3,RABEP2,SLC25A1,TP53TG1,ZNF580
ACOX3,ARSD,C9orf152,CAPN13,CCDC57,CYP2J2,DLG3,
EPHA1,FAM174B,GPR39,GUCY2D,IRX3,KIAA0319L,KLHL13,
LRRC48,MST1R,PIGO,PSD4,SEC16A,SPDEF,STYK1

AMPH,BPIFB2,CDH4,CLEC2A,CLEC2B,ELOVL2,BRINP3,
GUCY2D,KCNJ9,LRP1B,NR0B1,BPIFA1,REG1B,REG3A,
SDC4P,SERPINA12,SERPINA3,T,AGMO,TRIM17,ZIC1
AMPD1,C10orf91,C14orf183,HEXA-AS1,CD163L1,EMR4P,ENPP6,
FAM135B,GUCY2D,HTR7,IL31,LCN8,LHX1,MMP26,
LINC00112,OR6X1,PRM2,PSG7,PTCRA,SNORA11E,VSTM2A
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 GUCY2D
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA187; -.
Organism-specific databasesCTD 3000; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00131guanylate cyclase 2D, membrane (retina-specific)approved; nutraceuticalAdenosine monophosphate
DB00125guanylate cyclase 2D, membrane (retina-specific)approved; nutraceuticalL-Arginine
DB00155guanylate cyclase 2D, membrane (retina-specific)approved; nutraceuticalL-Citrulline
DB00435guanylate cyclase 2D, membrane (retina-specific)approvedNitric Oxide


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Cross referenced IDs for GUCY2D
* 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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