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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PPP1CB |
Basic gene info. | Gene symbol | PPP1CB |
Gene name | protein phosphatase 1, catalytic subunit, beta isozyme | |
Synonyms | HEL-S-80p|PP-1B|PP1B|PP1beta|PPP1CD | |
Cytomap | UCSC genome browser: 2p23 | |
Genomic location | chr2 :28974613-29025806 | |
Type of gene | protein-coding | |
RefGenes | NM_002709.2, NM_206876.1,NM_206877.1, | |
Ensembl id | ENSG00000213639 | |
Description | epididymis secretory sperm binding protein Li 80pprotein phosphatase 1, catalytic subunit, beta isoformprotein phosphatase 1, catalytic subunit, delta isoformprotein phosphatase 1-betaprotein phosphatase 1-deltaserine/threonine protein phosphatase PP | |
Modification date | 20141207 | |
dbXrefs | MIM : 600590 | |
HGNC : HGNC | ||
Ensembl : ENSG00000213639 | ||
HPRD : 11792 | ||
Vega : OTTHUMG00000152011 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PPP1CB | |
BioGPS: 5500 | ||
Gene Expression Atlas: ENSG00000213639 | ||
The Human Protein Atlas: ENSG00000213639 | ||
Pathway | NCI Pathway Interaction Database: PPP1CB | |
KEGG: PPP1CB | ||
REACTOME: PPP1CB | ||
ConsensusPathDB | ||
Pathway Commons: PPP1CB | ||
Metabolism | MetaCyc: PPP1CB | |
HUMANCyc: PPP1CB | ||
Regulation | Ensembl's Regulation: ENSG00000213639 | |
miRBase: chr2 :28,974,613-29,025,806 | ||
TargetScan: NM_002709 | ||
cisRED: ENSG00000213639 | ||
Context | iHOP: PPP1CB | |
cancer metabolism search in PubMed: PPP1CB | ||
UCL Cancer Institute: PPP1CB | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PPP1CB(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PPP1CB |
Familial Cancer Database: PPP1CB |
* 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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PPP1CB |
MedGen: PPP1CB (Human Medical Genetics with Condition) | |
ClinVar: PPP1CB | |
Phenotype | MGI: PPP1CB (International Mouse Phenotyping Consortium) |
PhenomicDB: PPP1CB |
Mutations for PPP1CB |
* 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 | PPP1CB | chr2 | 28988095 | 28988115 | PPP1CB | chr2 | 28989431 | 28989451 |
ovary | PPP1CB | chr2 | 28994324 | 28994344 | PLB1 | chr2 | 28817973 | 28817993 |
ovary | PPP1CB | chr2 | 29002047 | 29002067 | chr2 | 28921035 | 28921055 | |
ovary | PPP1CB | chr2 | 29012017 | 29012037 | PLB1 | chr2 | 28796085 | 28796105 |
ovary | PPP1CB | chr2 | 29023376 | 29023396 | chr2 | 177956392 | 177956412 | |
ovary | PPP1CB | chr2 | 29023382 | 29023402 | chr2 | 177956386 | 177956406 | |
ovary | PPP1CB | chr2 | 29025691 | 29025711 | chr2 | 177956664 | 177956684 |
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 PPP1CB 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 |
T06907 | RAPGEF1 | 1 | 172 | 9 | 134453266 | 134453437 | PPP1CB | 171 | 261 | 2 | 28974976 | 28999740 | |
BE170792 | PPP1CB | 1 | 144 | 2 | 29001864 | 29004706 | PPP1CB | 138 | 327 | 2 | 29016845 | 29022235 | |
BF811868 | PPP1CB | 1 | 273 | 2 | 29022698 | 29022970 | MIR548N | 266 | 340 | 2 | 179369171 | 179369245 | |
AI627549 | C1orf174 | 1 | 294 | 1 | 3805721 | 3806014 | PPP1CB | 287 | 430 | 2 | 29011954 | 29012097 | |
AL597156 | FOXP1 | 1 | 161 | 3 | 71630550 | 71630710 | PPP1CB | 161 | 436 | 2 | 28999716 | 29001817 | |
BP386903 | PDLIM1 | 1 | 105 | 10 | 97007367 | 97007471 | PPP1CB | 104 | 316 | 2 | 29023654 | 29023866 | |
CF139633 | PPP1CB | 35 | 235 | 2 | 29023709 | 29023909 | PPP1CB | 229 | 339 | 2 | 29023244 | 29023354 |
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=27) | (# total SNVs=5) |
(# total SNVs=0) | (# total SNVs=1) |
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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 |
chr2:29004610-29004610 | p.R141Q | 2 |
chr2:29011673-29011673 | p.Q248E | 2 |
chr2:28999779-28999779 | p.I39V | 2 |
chr2:29006839-29006839 | p.D196A | 1 |
chr2:29016810-29016810 | p.D276H | 1 |
chr2:28999824-28999824 | p.L54V | 1 |
chr2:29001882-29001882 | p.R131H | 1 |
chr2:29011533-29011533 | p.C201Y | 1 |
chr2:29016824-29016824 | p.G280G | 1 |
chr2:28999833-28999833 | p.P57S | 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 | 3 |   | 1 | 8 |   |   |   |   |   |   |   | 2 | 1 | 1 |   |   | 7 | 4 |   | 8 |
# mutation | 3 |   | 1 | 8 |   |   |   |   |   |   |   | 2 | 1 | 1 |   |   | 7 | 4 |   | 9 |
nonsynonymous SNV | 3 |   | 1 | 5 |   |   |   |   |   |   |   | 2 | 1 | 1 |   |   | 5 | 2 |   | 7 |
synonymous SNV |   |   |   | 3 |   |   |   |   |   |   |   |   |   |   |   |   | 2 | 2 |   | 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 |
chr2:29004610 | p.R141Q,PPP1CB | 2 |
chr2:29016792 | p.Q248E,PPP1CB | 1 |
chr2:28999833 | p.G90E,PPP1CB | 1 |
chr2:29004706 | p.V250A,PPP1CB | 1 |
chr2:29016803 | p.S99F,PPP1CB | 1 |
chr2:29001725 | p.V250V,PPP1CB | 1 |
chr2:29006808 | p.L106L,PPP1CB | 1 |
chr2:29016810 | p.N270Y,PPP1CB | 1 |
chr2:29001759 | p.K110T,PPP1CB | 1 |
chr2:29006809 | p.G273G,PPP1CB | 1 |
Other DBs for Point Mutations |
Copy Number for PPP1CB 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 PPP1CB |
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 |
ACTR2,ADAM17,ATL2,B3GNT5,EML4,FAM98A,GPN1, KCMF1,MEMO1,MSH2,PPP1CB,PPP3R1,PSME4,RAB10, SOS1,SPAST,UBXN2A,WDR43,YES1,YIPF4,YWHAQ | AASDHPPT,C15orf41,C5orf22,CNOT7,CUL3,DYRK1A,FBXO3, HINT3,HSF2,MOSPD1,NEDD1,NT5C3A,PPP1CB,PPP1R2, RAB10,RCHY1,RRP15,THAP9,TMEM65,UBE3A,VTA1 | ||||
ACTR2,ACTR3,AFTPH,C1D,DUSP11,LAPTM4A,MAP4K3, MMADHC,MOB4,PEX13,PIGK,PLEKHA3,PPP1CB,RAB1A, SEPT10,TANK,TMEM106B,TMEM87B,UGP2,YIPF4,YPEL5 | ARL8B,ASB8,ATP6V1H,GINM1,CCDC91,EFR3A,EIF4E3, LUZP6,MAP1LC3B,PPAP2A,PPP1CB,PRSS23,RAB7A,RIT1, RNF11,SHOC2,STRN3,TAB2,TAX1BP1,TLK1,TMEM30A |
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 PPP1CB |
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 |
DB01033 | protein phosphatase 1, catalytic subunit, beta isozyme | approved | Mercaptopurine | ||
DB00563 | protein phosphatase 1, catalytic subunit, beta isozyme | approved | Methotrexate |
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Cross referenced IDs for PPP1CB |
* 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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