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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PPM1L |
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Phenotypic Information for PPM1L(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PPM1L |
Familial Cancer Database: PPM1L |
* This gene is included in those cancer gene databases. |
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/ |
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REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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OMIM | 611931; gene. |
Orphanet | |
Disease | KEGG Disease: PPM1L |
MedGen: PPM1L (Human Medical Genetics with Condition) | |
ClinVar: PPM1L | |
Phenotype | MGI: PPM1L (International Mouse Phenotyping Consortium) |
PhenomicDB: PPM1L |
Mutations for PPM1L |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | PPM1L | chr3 | 160651807 | 160651827 | RSRC1 | chr3 | 157833355 | 157833375 |
ovary | PPM1L | chr3 | 160726646 | 160726666 | PPM1L | chr3 | 160730437 | 160730457 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PPM1L 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 |
AK025676 | RNF213 | 1 | 4031 | 17 | 78345693 | 78368151 | PPM1L | 4026 | 4050 | 3 | 160744481 | 160744505 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 3 |   | 1 | 1 |   |   |   |   | 4 |   | 2 |   |   |   |   |   |   | |||
GAIN (# sample) | 2 |   | 1 | 1 |   |   |   |   | 4 |   | 2 |   |   |   |   |   |   | |||
LOSS (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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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Stat. for Non-Synonymous SNVs (# total SNVs=32) | (# total SNVs=6) |
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(# total SNVs=0) | (# total SNVs=0) |
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* 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 |
chr3:160786805-160786805 | p.R136* | 6 |
chr3:160783285-160783285 | p.N44N | 3 |
chr3:160783254-160783254 | p.S34L | 2 |
chr3:160783226-160783226 | p.D25Y | 2 |
chr3:160783332-160783332 | p.R60K | 2 |
chr3:160786690-160786690 | p.N97N | 1 |
chr3:160783243-160783243 | p.N30N | 1 |
chr3:160786835-160786835 | p.H146Y | 1 |
chr3:160783336-160783336 | p.K61K | 1 |
chr3:160786714-160786714 | p.I105I | 1 |
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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 | 4 |   | 9 | 1 |   | 1 |   |   |   |   | 10 | 3 |   |   |   | 9 | 2 |   | 7 |
# mutation | 2 | 4 |   | 9 | 1 |   | 1 |   |   |   |   | 10 | 3 |   |   |   | 10 | 2 |   | 8 |
nonsynonymous SNV | 1 | 3 |   | 7 | 1 |   |   |   |   |   |   | 7 | 2 |   |   |   | 4 | 1 |   | 7 |
synonymous SNV | 1 | 1 |   | 2 |   |   | 1 |   |   |   |   | 3 | 1 |   |   |   | 6 | 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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* 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 |
chr3:160783332 | p.N209N | 2 |
chr3:160783243 | p.N223N | 2 |
chr3:160783285 | p.R239T | 2 |
chr3:160783293 | p.E79K | 1 |
chr3:160474330 | p.D204Y | 1 |
chr3:160786714 | p.F296L | 1 |
chr3:160679655 | p.E79E | 1 |
chr3:160783305 | p.D204E | 1 |
chr3:160474331 | p.S301A | 1 |
chr3:160786750 | p.K84N | 1 |
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* 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. |
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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 PPM1L |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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ASXL2,CNOT1,EML4,GAN,IPMK,KIAA0754,KIF1B, LOC284441,NMD3,NPAT,PAFAH1B2,PPM1L,RIF1,ROCK2, SHPRH,SLC30A6,STRN,UBXN7,USP34,ZDHHC20,ZFR | DIAPH2,EXOC6B,FOXN3,HIPK3,IGF2R,KIAA1715,LIMS1, LNPEP,MAN2A2,MPP6,NEK9,PARD3B,PCYT1A,PPM1L, RNF150,SAMD8,SETD7,TEAD1,TRIP12,USP9X,YPEL2 |
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AKAP13,CCDC186,C11orf30,CEP97,DAAM1,EP300,FAM168A, FAM63B,GTF2A1,KIAA1244,LRCH3,MAGI1,MAN1A2,N4BP2, NHLRC2,PPM1L,RNF168,STXBP5,TET2,TRIP11,ZFP91 | AHNAK,SOGA1,COL8A1,DLG5,ERC1,EVC,FN1, FYCO1,HDAC4,ITGA9,MACF1,NAV2,NFIC,NHSL2, PARD3B,PPM1L,PTPN14,ROR1,SACS,SYNE1,ZC3H13 |
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* 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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Pharmacological Information for PPM1L |
There's no related Drug. |
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Cross referenced IDs for PPM1L |
* 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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