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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GNB4 |
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Phenotypic Information for GNB4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GNB4 |
Familial Cancer Database: GNB4 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM |
Others | |
OMIM | 610863; gene. 615185; phenotype. |
Orphanet | 352670; Autosomal dominant intermediate Charcot-Marie-Tooth disease type F. |
Disease | KEGG Disease: GNB4 |
MedGen: GNB4 (Human Medical Genetics with Condition) | |
ClinVar: GNB4 | |
Phenotype | MGI: GNB4 (International Mouse Phenotyping Consortium) |
PhenomicDB: GNB4 |
Mutations for GNB4 |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | GNB4 | chr3 | 179137144 | 179137344 | chr3 | 180185698 | 180185898 | |
pancreas | GNB4 | chr3 | 179148289 | 179148309 | chr19 | 58276738 | 58276758 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GNB4 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BE155686 | SERPINB13 | 1 | 310 | 18 | 61264348 | 61264663 | GNB4 | 305 | 491 | 3 | 179134740 | 179134926 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 2 | 1 | 2 |   |   | 1 |   |   | 1 |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 2 | 1 | 2 |   |   | 1 |   |   | 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=29) | (# total SNVs=4) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr3:179131259-179131259 | p.R214R | 2 |
chr3:179123026-179123026 | p.D290N | 2 |
chr3:179123046-179123046 | p.R283H | 2 |
chr3:179131385-179131385 | p.E172K | 2 |
chr3:179132783-179132783 | p.P107L | 2 |
chr3:179137294-179137294 | p.? | 1 |
chr3:179123180-179123180 | p.G238G | 1 |
chr3:179131545-179131545 | p.L152S | 1 |
chr3:179119032-179119032 | p.S331Y | 1 |
chr3:179132797-179132797 | p.T102T | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 2 |   |   | 9 |   |   | 1 |   | 1 |   |   | 2 | 3 | 1 |   |   | 4 | 5 |   | 6 |
# mutation | 2 |   |   | 9 |   |   | 1 |   | 1 |   |   | 2 | 3 | 1 |   |   | 4 | 5 |   | 6 |
nonsynonymous SNV | 1 |   |   | 7 |   |   | 1 |   | 1 |   |   | 1 | 3 | 1 |   |   | 3 | 4 |   | 4 |
synonymous SNV | 1 |   |   | 2 |   |   |   |   |   |   |   | 1 |   |   |   |   | 1 | 1 |   | 2 |
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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr3:179123026 | p.D290N | 2 |
chr3:179131259 | p.D254H | 1 |
chr3:179132784 | p.P107S | 1 |
chr3:179119032 | p.F253C | 1 |
chr3:179143986 | p.T102T | 1 |
chr3:179131385 | p.A231G | 1 |
chr3:179132797 | p.L79L | 1 |
chr3:179119064 | p.I229I | 1 |
chr3:179131506 | p.Q75K | 1 |
chr3:179134313 | p.T223T | 1 |
Other DBs for Point Mutations |
Copy Number for GNB4 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 GNB4 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
ACTL6A,ANKRD36BP1,B3GNT5,COA7,CEP170,CORO1C,DCUN1D1, FNDC3B,FOXN2,GNB4,MFN1,OSBPL11,DESI2,QKI, RAP2A,ROCK2,SYNCRIP,YEATS2,YES1,ZCCHC11,ZNF639 | ARL15,CASC4,CHIC1,CTSO,DNAJC3,FAM91A1,GNB4, HSPA13,KRAS,MAGT1,MIER1,MOB1A,PRKAA1,RP2, SLC30A7,SOCS4,SPCS3,TGFBR1,TMED7,TMEM30A,TMTC3 |
C1S,CNRIP1,DSEL,ENTPD1,FBXL7,FSTL1,GNB4, HEG1,IL1R1,MAF,MRAS,MYO5A,NRP1,PKD2, PLEKHO2,PLXDC2,QKI,STARD8,TCF4,VIM,ZEB2 | ANGPT1,AP1S2,B3GALNT1,BLVRA,FAM229B,DUSP22,EIF5A2, FEZ1,GNB4,GUCY1B3,KIAA0895,LOC399959,LOC644538,SLC9B2, NME4,RAB23,RAB31,IFT22,RHOQ,TCEAL7,ZNF25 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for GNB4 |
There's no related Drug. |
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Cross referenced IDs for GNB4 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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