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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PIGL |
Basic gene info. | Gene symbol | PIGL |
Gene name | phosphatidylinositol glycan anchor biosynthesis, class L | |
Synonyms | CHIME | |
Cytomap | UCSC genome browser: 17p12-p11.2 | |
Genomic location | chr17 :16120508-16229573 | |
Type of gene | protein-coding | |
RefGenes | NM_004278.3, | |
Ensembl id | ENSG00000108474 | |
Description | N-acetylglucosaminyl-phosphatidylinositol de-N-acetylaseN-acetylglucosaminylphosphatidylinositol deacetylasePIG-Lphosphatidylinositol glycan, class Lphosphatidylinositol-glycan biosynthesis class L protein | |
Modification date | 20141207 | |
dbXrefs | MIM : 605947 | |
HGNC : HGNC | ||
Ensembl : ENSG00000108474 | ||
HPRD : 12071 | ||
Vega : OTTHUMG00000059346 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PIGL | |
BioGPS: 9487 | ||
Gene Expression Atlas: ENSG00000108474 | ||
The Human Protein Atlas: ENSG00000108474 | ||
Pathway | NCI Pathway Interaction Database: PIGL | |
KEGG: PIGL | ||
REACTOME: PIGL | ||
ConsensusPathDB | ||
Pathway Commons: PIGL | ||
Metabolism | MetaCyc: PIGL | |
HUMANCyc: PIGL | ||
Regulation | Ensembl's Regulation: ENSG00000108474 | |
miRBase: chr17 :16,120,508-16,229,573 | ||
TargetScan: NM_004278 | ||
cisRED: ENSG00000108474 | ||
Context | iHOP: PIGL | |
cancer metabolism search in PubMed: PIGL | ||
UCL Cancer Institute: PIGL | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PIGL(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PIGL |
Familial Cancer Database: PIGL |
* 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_METABOLISM_OF_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PIGL |
MedGen: PIGL (Human Medical Genetics with Condition) | |
ClinVar: PIGL | |
Phenotype | MGI: PIGL (International Mouse Phenotyping Consortium) |
PhenomicDB: PIGL |
Mutations for PIGL |
* 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 |
large_intestine | PIGL | chr17 | 16138070 | 16138070 | PIGL | chr17 | 16162625 | 16162625 |
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 PIGL 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 |
BE706180 | FN1 | 10 | 157 | 2 | 216264037 | 216269224 | PIGL | 155 | 317 | 17 | 16167728 | 16167890 |
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 | 4 |   |   | 1 |   |   |   |   |   |   |   |   |   |   | 3 |   |   | |||
GAIN (# sample) | 2 |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) | 2 |   |   |   |   |   |   |   |   |   |   |   |   |   | 3 |   |   |
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=15) | (# total SNVs=3) |
(# 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 |
chr17:16120764-16120764 | p.C75S | 1 |
chr17:16221127-16221127 | p.R189G | 1 |
chr17:16137283-16137283 | p.? | 1 |
chr17:16221134-16221134 | p.Y191C | 1 |
chr17:16137299-16137299 | p.Q84* | 1 |
chr17:16221154-16221154 | p.P198S | 1 |
chr17:16120544-16120544 | p.E2K | 1 |
chr17:16137360-16137360 | p.S104C | 1 |
chr17:16221155-16221155 | p.P198L | 1 |
chr17:16120548-16120548 | p.A3E | 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 | 1 |   |   | 1 |   |   | 1 |   | 2 |   |   | 3 | 1 |   |   |   | 2 | 2 |   | 2 |
# mutation | 1 |   |   | 1 |   |   | 1 |   | 2 |   |   | 3 | 1 |   |   |   | 2 | 2 |   | 2 |
nonsynonymous SNV | 1 |   |   |   |   |   |   |   | 2 |   |   | 3 | 1 |   |   |   | 1 | 2 |   | 1 |
synonymous SNV |   |   |   | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   | 1 |   |   | 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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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 |
chr17:16203255 | p.K220Q | 1 |
chr17:16216926 | p.R242Q | 1 |
chr17:16220021 | p.E2K | 1 |
chr17:16120544 | p.V13A | 1 |
chr17:16221127 | p.V13V | 1 |
chr17:16120578 | p.I47I | 1 |
chr17:16221154 | p.A48P | 1 |
chr17:16120579 | p.S104C | 1 |
chr17:16221220 | p.H126H | 1 |
chr17:16120681 | p.R129G | 1 |
Other DBs for Point Mutations |
Copy Number for PIGL 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 PIGL |
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 |
AHSA2,ATPAF2,CENPV,CNTROB,DPH1,DRG2,KCNAB3, LENG8,LOC338799,MAPK8IP3,MYO15B,NEURL4,NLGN2,PAN2, PFAS,PIGL,SCX,SGSM2,TTLL3,TUBGCP6,ZSWIM7 | CARF,BMS1P4,BTAF1,DNHD1,L3MBTL1,LOC100131434,LOC100272228, LOC440944,LOC646471,MSH5,MYSM1,NKTR,PAN2,PDXDC2P, PIGL,STAG3L3,TRIM66,CFAP70,UBE2Q2P1,WDR27,XIST |
ACADVL,ALKBH6,SNHG15,CDK5RAP3,CENPV,CYP2R1,DRG2, INCA1,PAN2,PIGL,POLR2J4,RPAIN,SNHG10,SNHG12, SNHG3,SUV420H2,TEC,TMEM160,EMC6,TRMT1,ZSWIM7 | RSRP1,CAPN10,CDK5RAP3,CHKB-CPT1B,GIPR,CLUHP3,KIFC2, LOC100131434,LOC100272228,LOC642846,NAA40,NOXA1,NSUN5P1,NSUN5P2, PDXDC2P,PIGL,PLEKHM1P,RHOT2,SNHG12,ZNF276,ZNF513 |
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 PIGL |
There's no related Drug. |
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Cross referenced IDs for PIGL |
* 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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