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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GPC5 |
Basic gene info. | Gene symbol | GPC5 |
Gene name | glypican 5 | |
Synonyms | - | |
Cytomap | UCSC genome browser: 13q32 | |
Genomic location | chr13 :92050934-93519487 | |
Type of gene | protein-coding | |
RefGenes | NM_004466.5, | |
Ensembl id | ENSG00000179399 | |
Description | bA93M14.1glypican proteoglycan 5glypican-5 | |
Modification date | 20141207 | |
dbXrefs | MIM : 602446 | |
HGNC : HGNC | ||
Ensembl : ENSG00000179399 | ||
HPRD : 03902 | ||
Vega : OTTHUMG00000017200 | ||
Protein | UniProt: P78333 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GPC5 | |
BioGPS: 2262 | ||
Gene Expression Atlas: ENSG00000179399 | ||
The Human Protein Atlas: ENSG00000179399 | ||
Pathway | NCI Pathway Interaction Database: GPC5 | |
KEGG: GPC5 | ||
REACTOME: GPC5 | ||
ConsensusPathDB | ||
Pathway Commons: GPC5 | ||
Metabolism | MetaCyc: GPC5 | |
HUMANCyc: GPC5 | ||
Regulation | Ensembl's Regulation: ENSG00000179399 | |
miRBase: chr13 :92,050,934-93,519,487 | ||
TargetScan: NM_004466 | ||
cisRED: ENSG00000179399 | ||
Context | iHOP: GPC5 | |
cancer metabolism search in PubMed: GPC5 | ||
UCL Cancer Institute: GPC5 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for GPC5(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GPC5 |
Familial Cancer Database: GPC5 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in BLCA 6, |
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, 6 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12965.html, 7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_CARBOHYDRATES |
Others | |
OMIM | 602446; gene. |
Orphanet | |
Disease | KEGG Disease: GPC5 |
MedGen: GPC5 (Human Medical Genetics with Condition) | |
ClinVar: GPC5 | |
Phenotype | MGI: GPC5 (International Mouse Phenotyping Consortium) |
PhenomicDB: GPC5 |
Mutations for GPC5 |
* 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 |
breast | GPC5 | chr13 | 93450097 | 93450097 | chr8 | 138327667 | 138327667 | |
haematopoietic_and_lymphoid_tissue | GPC5 | chr13 | 92688884 | 92688884 | GPC5 | chr13 | 92688884 | 92688884 |
haematopoietic_and_lymphoid_tissue | GPC5 | chr13 | 93187498 | 93187498 | GPC5 | chr13 | 93187498 | 93187498 |
ovary | GPC5 | chr13 | 92221030 | 92221050 | GPC5 | chr13 | 92146414 | 92146434 |
ovary | GPC5 | chr13 | 92248228 | 92248248 | GPC5 | chr13 | 92250187 | 92250207 |
ovary | GPC5 | chr13 | 92279355 | 92279375 | chr21 | 25411358 | 25411378 | |
ovary | GPC5 | chr13 | 92332369 | 92332389 | GPC5 | chr13 | 92347896 | 92347916 |
ovary | GPC5 | chr13 | 92396551 | 92396571 | GPC5 | chr13 | 92396630 | 92396650 |
ovary | GPC5 | chr13 | 92622424 | 92622444 | GPC5 | chr13 | 92623711 | 92623731 |
ovary | GPC5 | chr13 | 92879888 | 92879908 | chr11 | 76265513 | 76265533 | |
ovary | GPC5 | chr13 | 93029950 | 93029970 | ASIC2 | chr17 | 31343849 | 31343869 |
ovary | GPC5 | chr13 | 93143700 | 93143720 | CADPS | chr3 | 62751151 | 62751171 |
ovary | GPC5 | chr13 | 93190946 | 93191146 | chr6 | 94275073 | 94275273 | |
ovary | GPC5 | chr13 | 93305091 | 93305111 | GPC5 | chr13 | 93306114 | 93306134 |
pancreas | GPC5 | chr13 | 92410079 | 92410099 | GPC5 | chr13 | 92414289 | 92414309 |
pancreas | GPC5 | chr13 | 92802781 | 92802801 | GPC5 | chr13 | 92831832 | 92831852 |
pancreas | GPC5 | chr13 | 92806584 | 92806604 | GPC5 | chr13 | 92957033 | 92957053 |
pancreas | GPC5 | chr13 | 93356204 | 93356224 | GPC5 | chr13 | 93356314 | 93356334 |
pancreas | GPC5 | chr13 | 93457098 | 93457118 | GPC5 | chr13 | 93470158 | 93470178 |
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 GPC5 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 |
DW467550 | GPC5 | 17 | 137 | 13 | 93476060 | 93476181 | GPC5 | 138 | 345 | 13 | 93473461 | 93473668 | |
DW446998 | GPC5 | 17 | 137 | 13 | 93476060 | 93476181 | GPC5 | 138 | 214 | 13 | 93473461 | 93473537 | |
AI827689 | GPC5 | 2 | 414 | 13 | 92992050 | 93004461 | CDYL | 412 | 501 | 6 | 4716028 | 4716117 |
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 | 7 | 3 |   |   | 2 | 2 | 6 |   | 9 |   | 3 |   |   | 3 | 4 | 2 | 2 | |||
GAIN (# sample) | 7 | 3 |   |   | 1 | 1 | 6 |   | 5 |   | 1 |   |   | 3 | 4 |   | 2 | |||
LOSS (# sample) |   |   |   |   | 1 | 1 |   |   | 4 |   | 2 |   |   | 1 |   | 2 |   |
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=111) | (# total SNVs=20) |
(# total SNVs=0) | (# total SNVs=3) |
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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 |
chr13:92101015-92101015 | p.G55E | 4 |
chr13:92345629-92345629 | p.P172S | 3 |
chr13:93518536-93518536 | p.W521* | 3 |
chr13:92380805-92380805 | p.R347H | 3 |
chr13:92101156-92101156 | p.R102Q | 3 |
chr13:92345703-92345703 | p.M196I | 2 |
chr13:92797119-92797119 | p.E480K | 2 |
chr13:92346074-92346074 | p.H320L | 2 |
chr13:92345764-92345764 | p.R217W | 2 |
chr13:92346004-92346004 | p.R297W | 2 |
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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 | 5 | 8 |   | 13 | 1 |   | 10 |   | 4 | 1 |   | 16 | 11 | 3 |   |   | 26 | 19 | 1 | 14 |
# mutation | 5 | 8 |   | 13 | 1 |   | 11 |   | 4 | 1 |   | 20 | 11 | 3 |   |   | 29 | 19 | 1 | 18 |
nonsynonymous SNV | 4 | 5 |   | 11 |   |   | 8 |   | 4 | 1 |   | 13 | 11 | 3 |   |   | 23 | 13 | 1 | 15 |
synonymous SNV | 1 | 3 |   | 2 | 1 |   | 3 |   |   |   |   | 7 |   |   |   |   | 6 | 6 |   | 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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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 |
chr13:92380805 | p.R347H | 3 |
chr13:92345909 | p.P259L | 2 |
chr13:92345703 | p.A265V | 2 |
chr13:92797193 | p.R210K | 2 |
chr13:92797198 | p.Q83H | 2 |
chr13:92345629 | p.R217W | 2 |
chr13:92380859 | p.E480K | 2 |
chr13:92345744 | p.R102Q | 2 |
chr13:92101100 | p.P172S | 2 |
chr13:93518546 | p.C504C | 2 |
Other DBs for Point Mutations |
Copy Number for GPC5 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 GPC5 |
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 |
ATP1A4,ACSM6,C11orf94,MROH7,C2orf27B,CASQ1,CHIA, DEFB109P1B,GPC5,HERC1,HHEX,KCNJ8,LOC149620,LOC285780, LOC340508,MS4A8,OR52B4,OR8B8,PROK1,SKINTL,TSPAN6 | ADAM22,ADRB3,AFF2,ALDOB,C1orf198,CADM2,CES1P1, CRIM1,DAAM1,GNAL,GPC5,GPLD1,KIAA0040,NECAB1, NLGN1,NRCAM,PCLO,PTPRQ,SCIN,TMEM64,YAP1 |
AKR1C8P,ATP12A,C3P1,CCDC85A,CD7,CELF4,CHST9, DIO1,FAM138D,FLJ35024,FOXB1,GPC5,GSTA3,HOXC12, KCNB2,MS4A15,PAK3,RDH8,S100A7A,SERPIND1,SPDYC | CCDC181,CACNG4,CDK5R2,CELF3,CELF6,CPLX2,ELAVL4, ETV1,GNG3,GPC5,HMP19,OLFM3,PABPC1L2B,PIRT, RANBP3L,SCG2,SCG3,SLC6A15,SULT4A1,SYT9,UCHL1 |
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 GPC5 |
There's no related Drug. |
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Cross referenced IDs for GPC5 |
* 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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