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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GCAT |
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Phenotypic Information for GCAT(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GCAT |
Familial Cancer Database: GCAT |
* 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 | |
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GCAT |
MedGen: GCAT (Human Medical Genetics with Condition) | |
ClinVar: GCAT | |
Phenotype | MGI: GCAT (International Mouse Phenotyping Consortium) |
PhenomicDB: GCAT |
Mutations for GCAT |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GCAT 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 |
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 |   |   |   |   |   |   |   |   |   |   | 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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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=23) | (# total SNVs=9) |
(# total SNVs=1) | (# 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 |
chr22:38204089-38204089 | p.R39C | 3 |
chr22:38211771-38211771 | p.A306S | 2 |
chr22:38211173-38211173 | p.S206F | 2 |
chr22:38211196-38211196 | p.L214L | 1 |
chr22:38204144-38204144 | p.H57L | 1 |
chr22:38211724-38211724 | p.R290P | 1 |
chr22:38209491-38209491 | p.A151S | 1 |
chr22:38212603-38212603 | p.V380M | 1 |
chr22:38211243-38211243 | p.F229F | 1 |
chr22:38206039-38206039 | p.L68F | 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 |   | 3 | 2 |   | 3 |   |   |   | 1 | 6 | 2 |   |   |   | 8 | 3 |   | 2 |
# mutation |   | 2 |   | 3 | 2 |   | 3 |   |   |   | 1 | 6 | 2 |   |   |   | 9 | 3 |   | 2 |
nonsynonymous SNV |   | 2 |   | 1 | 1 |   | 3 |   |   |   |   | 6 | 1 |   |   |   | 4 | 3 |   |   |
synonymous SNV |   |   |   | 2 | 1 |   |   |   |   |   | 1 |   | 1 |   |   |   | 5 |   |   | 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 |
chr22:38211771 | p.I111T,GCAT | 1 |
chr22:38206091 | p.P306S,GCAT | 1 |
chr22:38212689 | p.F434F,GCAT | 1 |
chr22:38211196 | p.L167L,GCAT | 1 |
chr22:38212210 | p.L307P,GCAT | 1 |
chr22:38208989 | p.F168S,GCAT | 1 |
chr22:38211243 | p.V308L,GCAT | 1 |
chr22:38212212 | p.A177V,GCAT | 1 |
chr22:38208991 | p.R316P,GCAT | 1 |
chr22:38211274 | p.D190D,GCAT | 1 |
Other DBs for Point Mutations |
Copy Number for GCAT 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 GCAT |
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 |
ANKRD54,SMDT1,DGCR6,DGCR6L,GCAT,GGA1,HSCB, IFT27,MCAT,MPST,NHP2L1,NOL12,PICK1,RHBDD3, RPS19BP1,SDF2L1,THAP7,TOMM22,TXN2,UQCR10,ZMAT5 | APEH,RITA1,CECR5,COQ4,DDX49,DHPS,EXOSC5, FARSA,GCAT,MCAT,MFSD3,MLST8,NHP2,NUDT16L1, RPL8,RUVBL2,MIEF2,THOP1,TMEM134,TMEM141,TRUB2 | ||||
ATPAF2,CENPM,DGCR6L,DHRS13,ENDOG,F12,GCAT, HSCB,DANCR,NAA38,MCAT,MTFP1,NPM3,POLR2L, PUSL1,SDF2L1,TIMM13,TMEM52,TSPO,TXN2,UQCR10 | AHCY,CD320,ECSIT,EIF4EBP1,EXOSC5,FBXW9,GCAT, HIST3H2A,LAGE3,MLST8,MMACHC,MRPL37,MRPL4,MRPS18A, MRPS2,PAFAH1B3,PPP1R1B,PRMT7,SFXN4,TARBP2,TIMM13 |
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 GCAT |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00114 | glycine C-acetyltransferase | nutraceutical | Pyridoxal Phosphate | ||
DB00145 | glycine C-acetyltransferase | approved; nutraceutical | Glycine |
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Cross referenced IDs for GCAT |
* 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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