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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PNLIPRP1 |
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Phenotypic Information for PNLIPRP1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PNLIPRP1 |
Familial Cancer Database: PNLIPRP1 |
* 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_GLYCEROLIPID_METABOLISM |
Mutations for PNLIPRP1 |
* 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 | PNLIPRP1 | chr10 | 118368476 | 118368496 | chr10 | 118369355 | 118369375 |
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 PNLIPRP1 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 |
There's no copy number variation information in COSMIC data for this gene. |
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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=66) | (# total SNVs=20) |
(# 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 |
chr10:118363546-118363546 | p.W356C | 3 |
chr10:118357393-118357393 | p.D210N | 3 |
chr10:118360655-118360655 | p.R335S | 2 |
chr10:118354325-118354325 | p.N138K | 2 |
chr10:118354250-118354250 | p.F113F | 2 |
chr10:118351283-118351283 | p.G17E | 2 |
chr10:118359658-118359658 | p.S305F | 2 |
chr10:118357378-118357378 | p.E205* | 2 |
chr10:118354277-118354277 | p.C122C | 2 |
chr10:118355811-118355811 | p.T184I | 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 | 4 | 4 |   | 5 |   |   | 6 |   | 1 |   |   | 14 | 5 | 1 |   | 1 | 11 | 5 |   | 4 |
# mutation | 4 | 4 |   | 5 |   |   | 6 |   | 1 |   |   | 15 | 7 | 1 |   | 1 | 15 | 5 |   | 6 |
nonsynonymous SNV | 4 | 3 |   | 4 |   |   | 5 |   |   |   |   | 9 | 4 | 1 |   |   | 10 | 4 |   | 6 |
synonymous SNV |   | 1 |   | 1 |   |   | 1 |   | 1 |   |   | 6 | 3 |   |   | 1 | 5 | 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 |
chr10:118354250 | p.F113F | 3 |
chr10:118359629 | p.P295P | 2 |
chr10:118359630 | p.D296N | 2 |
chr10:118354289 | p.R90R | 1 |
chr10:118360618 | p.H166Y | 1 |
chr10:118355782 | p.S261F | 1 |
chr10:118365010 | p.T399T | 1 |
chr10:118351422 | p.F96I | 1 |
chr10:118357567 | p.I168I | 1 |
chr10:118354329 | p.W270L | 1 |
Other DBs for Point Mutations |
Copy Number for PNLIPRP1 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 PNLIPRP1 |
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 |
BTBD17,CABS1,PPP1R17,CELA2B,CELA3A,CELA3B,CLPS, CPA1,CPA2,CTRB1,CTRB2,CTRC,PLA2G1B,PNLIP, PNLIPRP1,REG1B,REG1P,REG3A,SCGB3A1,SYCN,TBR1 | ARGFX,LINC00293,BTLA,C9orf57,CACNG2,FCAMR,H1FOO, LILRP2,LOC283663,NEUROG1,OR5B3,OR5C1,OR8G2,OR8I2, OR8K1,PNLIPRP1,PRNT,SMEK3P,TCL6,ZIM3,ZNF679 |
AMY2A,C11orf40,CELA2A,CELA2B,CELA3A,CELA3B,CLPS, CPA1,CTRB1,CTRB2,CTRC,CYP2A6,DUSP15,OPRM1, PDYN,PLA2G1B,PNLIP,PNLIPRP1,PNLIPRP2,SYCN,ZNF280B | ARHGAP36,B3GALT5-AS1,SPTSSB,CLDN8,CRYBA2,CTSE,FBXO25, FRZB,GGT7,GP2,HEPACAM2,IL1R2,KLK3,LOC284578, NRAP,PNLIPRP1,RESP18,RETNLB,RIMS4,SCGB2A1,ZNF613 |
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 PNLIPRP1 |
There's no related Drug. |
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Cross referenced IDs for PNLIPRP1 |
* 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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