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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PC |
Basic gene info. | Gene symbol | PC |
Gene name | pyruvate carboxylase | |
Synonyms | PCB | |
Cytomap | UCSC genome browser: 11q13.4-q13.5 | |
Genomic location | chr11 :66615996-66675340 | |
Type of gene | protein-coding | |
RefGenes | NM_000920.3, NM_001040716.1,NM_022172.2, | |
Ensembl id | ENSG00000173599 | |
Description | pyruvate carboxylase, mitochondrialpyruvic carboxylase | |
Modification date | 20141219 | |
dbXrefs | MIM : 608786 | |
HGNC : HGNC | ||
Ensembl : ENSG00000173599 | ||
HPRD : 02032 | ||
Vega : OTTHUMG00000167099 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PC | |
BioGPS: 5091 | ||
Gene Expression Atlas: ENSG00000173599 | ||
The Human Protein Atlas: ENSG00000173599 | ||
Pathway | NCI Pathway Interaction Database: PC | |
KEGG: PC | ||
REACTOME: PC | ||
ConsensusPathDB | ||
Pathway Commons: PC | ||
Metabolism | MetaCyc: PC | |
HUMANCyc: PC | ||
Regulation | Ensembl's Regulation: ENSG00000173599 | |
miRBase: chr11 :66,615,996-66,675,340 | ||
TargetScan: NM_000920 | ||
cisRED: ENSG00000173599 | ||
Context | iHOP: PC | |
cancer metabolism search in PubMed: PC | ||
UCL Cancer Institute: PC | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PC(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PC |
Familial Cancer Database: PC |
* 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_PYRUVATE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PC |
MedGen: PC (Human Medical Genetics with Condition) | |
ClinVar: PC | |
Phenotype | MGI: PC (International Mouse Phenotyping Consortium) |
PhenomicDB: PC |
Mutations for PC |
* 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 |
There's no inter-chromosomal structural variation. |
- 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 | PC | chr11 | 66649381 | 66649401 | C11orf80 | chr11 | 66607747 | 66607767 |
pancreas | PC | chr11 | 66658803 | 66658823 | SHANK2 | chr11 | 70513932 | 70513952 |
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 PC 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 |
AI015900 | PC | 1 | 211 | 11 | 66625050 | 66625262 | SLC9A8 | 210 | 263 | 20 | 48507827 | 48507880 | |
BF894585 | PC | 28 | 87 | 11 | 66633761 | 66633820 | MIEN1 | 81 | 386 | 17 | 37885703 | 37886518 | |
AI080632 | PC | 1 | 213 | 11 | 66625050 | 66625262 | SLC9A8 | 212 | 517 | 20 | 48507575 | 48507880 | |
BF891034 | PC | 1 | 226 | 11 | 66617167 | 66617473 | PC | 220 | 316 | 11 | 66617080 | 66617176 |
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 | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 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=85) | (# total SNVs=37) |
(# total SNVs=5) | (# 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 |
chr11:66618550-66618550 | p.E728E | 4 |
chr11:66619987-66619987 | p.R583H | 3 |
chr11:66617203-66617203 | p.S1009L | 3 |
chr11:66617766-66617766 | p.M881I | 3 |
chr11:66620051-66620051 | p.G562W | 3 |
chr11:66638892-66638892 | p.F127F | 2 |
chr11:66616434-66616434 | p.R1158H | 2 |
chr11:66639505-66639505 | p.V42V | 2 |
chr11:66618514-66618514 | p.I740M | 2 |
chr11:66638919-66638919 | p.Y118Y | 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 | 3 | 4 | 1 | 19 | 2 |   | 9 |   | 2 | 2 | 1 | 9 | 4 | 2 |   |   | 13 | 10 | 1 | 13 |
# mutation | 3 | 4 | 1 | 19 | 2 |   | 9 |   | 2 | 2 | 1 | 10 | 4 | 2 |   |   | 14 | 12 | 1 | 19 |
nonsynonymous SNV | 1 | 4 | 1 | 12 | 2 |   | 7 |   | 1 | 2 |   | 5 | 1 |   |   |   | 11 | 9 | 1 | 11 |
synonymous SNV | 2 |   |   | 7 |   |   | 2 |   | 1 |   | 1 | 5 | 3 | 2 |   |   | 3 | 3 |   | 8 |
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 |
chr11:66618550 | p.E728E,PC | 4 |
chr11:66617476 | p.R1158H,PC | 2 |
chr11:66619987 | p.L601L,PC | 2 |
chr11:66638919 | p.M881I,PC | 2 |
chr11:66617874 | p.R583H,PC | 2 |
chr11:66619932 | p.Y118Y,PC | 2 |
chr11:66639309 | p.Y845Y,PC | 2 |
chr11:66620276 | p.V944M,PC | 2 |
chr11:66639505 | p.T57M,PC | 2 |
chr11:66617766 | p.P515P,PC | 2 |
Other DBs for Point Mutations |
Copy Number for PC 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 PC |
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 |
ANAPC11,ARHGDIA,ARL16,ASPSCR1,C17orf89,OXLD1,CCDC137, DCXR,DUS1L,FAM195B,GPS1,HGS,LRRC45,MRPL12, MRPL38,PCYT2,RAC3,RFNG,SIRT7,SLC25A10,STRA13 | ALDH1L1,ASS1,C17orf53,IZUMO4,C20orf27,APMAP,ECHDC3, FASN,GCDH,GLUL,GLYCTK,MPST,NDRG4,PC, PCYT2,PMM1,PXMP2,RASL10B,SHMT1,SLC25A1,TMEM120A | ||||
ATP5D,UQCC3,COX8A,DCXR,DUS1L,GPS1,LRRC45, MRPL12,MRPL38,NAPRT,NDUFS8,NT5C,PCYT2,PYCR1, RFNG,RNF126,SIRT7,SLC25A10,SLC25A39,SURF2,TSEN54 | AGMAT,AIMP2,AKR7A3,DNPH1,CENPV,CISD3,COQ4, FAM195A,FAM35A,FAM35BP,HADH,IMP3,MTCH2,NDUFC2, OXNAD1,PCYT2,PRR5,SHMT1,SLC25A10,SUCLG1,TRAF4 |
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 PC |
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 |
DB00119 | pyruvate carboxylase | approved; nutraceutical | Pyruvic acid | ||
DB00121 | pyruvate carboxylase | approved; nutraceutical | Biotin | ||
DB07497 | pyruvate carboxylase | experimental | 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL |
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Cross referenced IDs for PC |
* 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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