Cancer Cell Metabolism Gene Database

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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 GUCY1B3
Basic gene info.Gene symbolGUCY1B3
Gene nameguanylate cyclase 1, soluble, beta 3
SynonymsGC-S-beta-1|GC-SB3|GUC1B3|GUCB3|GUCSB3|GUCY1B1
CytomapUCSC genome browser: 4q31.3-q33
Genomic locationchr4 :156680125-156728783
Type of geneprotein-coding
RefGenesNM_000857.3,
NM_001291951.1,NM_001291952.1,NM_001291953.1,NM_001291954.1,
NM_001291955.1,
Ensembl idENSG00000061918
DescriptionGCS-beta-1GCS-beta-3guanylate cyclase soluble subunit beta-1guanylate cyclase soluble subunit beta-3soluble guanylate cyclase small subunit
Modification date20141207
dbXrefs MIM : 139397
HGNC : HGNC
Ensembl : ENSG00000061918
HPRD : 00769
Vega : OTTHUMG00000161698
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GUCY1B3
BioGPS: 2983
Gene Expression Atlas: ENSG00000061918
The Human Protein Atlas: ENSG00000061918
PathwayNCI Pathway Interaction Database: GUCY1B3
KEGG: GUCY1B3
REACTOME: GUCY1B3
ConsensusPathDB
Pathway Commons: GUCY1B3
MetabolismMetaCyc: GUCY1B3
HUMANCyc: GUCY1B3
RegulationEnsembl's Regulation: ENSG00000061918
miRBase: chr4 :156,680,125-156,728,783
TargetScan: NM_000857
cisRED: ENSG00000061918
ContextiHOP: GUCY1B3
cancer metabolism search in PubMed: GUCY1B3
UCL Cancer Institute: GUCY1B3
Assigned class in ccmGDBC

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Phenotypic Information for GUCY1B3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GUCY1B3
Familial Cancer Database: GUCY1B3
* 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
Orphanet
DiseaseKEGG Disease: GUCY1B3
MedGen: GUCY1B3 (Human Medical Genetics with Condition)
ClinVar: GUCY1B3
PhenotypeMGI: GUCY1B3 (International Mouse Phenotyping Consortium)
PhenomicDB: GUCY1B3

Mutations for GUCY1B3
* 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
breastGUCY1B3chr4156696873156697273chr4156885758156886158
pancreasGUCY1B3chr4156700598156700618GLRBchr4158082577158082597
pancreasGUCY1B3chr4156717766156717786ARNT2chr158081267880812698
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 GUCY1B3 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 # sample1                
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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=55)
Stat. for Synonymous SNVs
(# total SNVs=16)
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
chr4:156710914-156710914p.R116C3
chr4:156725805-156725805p.R539*2
chr4:156716530-156716530p.S255L2
chr4:156710916-156710916p.R116R2
chr4:156721098-156721098p.T349T2
chr4:156710952-156710952p.G128G2
chr4:156721101-156721101p.R350R2
chr4:156698728-156698728p.F77L2
chr4:156725753-156725753p.I521M2
chr4:156711052-156711052p.I162V1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22114  3 11 732 189 5
# mutation22116  3 11 732 1910 7
nonsynonymous SNV21 15  3 11 53   68 6
synonymous SNV 111       2 2 132 1
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
chr4:156710914p.S187L,GUCY1B32
chr4:156716530p.R48C,GUCY1B32
chr4:156716538p.G23C,GUCY1B31
chr4:156726280p.I355M1
chr4:156698713p.K491R,GUCY1B31
chr4:156721176p.T42I,GUCY1B31
chr4:156711063p.S187S,GUCY1B31
chr4:156723647p.R339Q,GUCY1B31
chr4:156716546p.G492R,GUCY1B31
chr4:156726310p.R190C,GUCY1B31

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 GUCY1B3 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 GUCY1B3

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

CALD1,CCDC102B,CDH6,CHSY3,COL15A1,COL4A1,GPR116,
GUCY1A3,GUCY1B3,HEG1,ITGA1,ITGAV,JAZF1,LAMA4,
NID1,NID2,NRP1,PCDH17,PRRX1,SH2B3,ZEB2
CARD8,CDH6,CLIC4,CPNE8,DPY19L1,EIF5A2,EMCN,
FLRT2,GUCY1B3,IL33,KCTD12,LBR,LRCH2,MFAP3,
PDE1A,DESI2,RAB8B,SEPT7,SGMS1,SGTB,SLFN11

BNC2,CALD1,CNRIP1,CYYR1,DZIP1,ELOVL4,FBXL7,
FERMT2,GUCY1A3,GUCY1B3,LDB2,LPHN2,MPDZ,MSRB3,
MYCT1,PABPC5,RHOJ,SGCD,TEK,TSHZ3,ZEB1
CLMP,BAG2,FEZ1,GUCY1A3,GUCY1B3,LOC644538,LRCH2,
PABPC5,PLEKHO1,PLN,PRDM8,PRNP,PTBP2,RAB23,
RAB31,RERG,RHOQ,RND2,SCRG1,TMEM55A,ZNF25
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 GUCY1B3
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
DB00171guanylate cyclase 1, soluble, beta 3approved; nutraceuticalAdenosine triphosphate
DB00125guanylate cyclase 1, soluble, beta 3approved; nutraceuticalL-Arginine
DB00155guanylate cyclase 1, soluble, beta 3approved; nutraceuticalL-Citrulline
DB00435guanylate cyclase 1, soluble, beta 3approvedNitric Oxide


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Cross referenced IDs for GUCY1B3
* 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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