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| Phenotypic Information (metabolism pathway, cancer, disease, phenome) |
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| Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG |
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| Gene Summary for PHOSPHO1 |
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| Phenotypic Information for PHOSPHO1(metabolism pathway, cancer, disease, phenome) |
 Cancer Description | |
| Cancer | CGAP: PHOSPHO1 |
| Familial Cancer Database: PHOSPHO1 | |
| * 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_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS | |
| Mutations for PHOSPHO1 |
| * 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 |
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| - For Inter-chromosomal Variations |
| There's no inter-chromosomal structural variation. |
| - For Intra-chromosomal Variations |
| There's no intra-chromosomal structural variation. |
| Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
| 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 PHOSPHO1 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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: Non-synonymous mutation, 
: Synonymous mutation, Circle size denotes number of samples. |
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| Somatic Mutation Counts per Tissue in COSMIC data |
| Stat. for Non-Synonymous SNVs (# total SNVs=4) | (# total SNVs=3) |
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(# 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 |
| chr17:47301695-47301695 | p.E239E | 1 |
| chr17:47301805-47301805 | p.D203H | 1 |
| chr17:47301826-47301826 | p.E196* | 1 |
| chr17:47301913-47301914 | p.H166fs*>102 | 1 |
| chr17:47301990-47301990 | p.L141R | 1 |
| chr17:47302012-47302012 | p.R134C | 1 |
| chr17:47302132-47302132 | p.E94K | 1 |
| chr17:47302153-47302153 | p.R87W | 1 |
| chr17:47302164-47302164 | p.G83V | 1 |
| chr17:47302349-47302349 | p.A21A | 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 | |||||||||||||||||||
| # mutation | 1 | |||||||||||||||||||
| nonsynonymous SNV | 1 | |||||||||||||||||||
| synonymous SNV |
| 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 |
| chr17:47302012 | p.R159C,PHOSPHO1 | 1 |
| Other DBs for Point Mutations |
| Copy Number for PHOSPHO1 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. |
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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 PHOSPHO1 |
| 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. |
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| 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. |
: Open all plots for all cancer types
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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 |
: Open all plots for all cancer types
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| ACAN,AOC2,BGLAP,CDH15,DMP1,ENPEP,FXYD4, IBSP,IFITM5,MEPE,MRC2,NOS2,P4HA2,PANX3, PHOSPHO1,PRELP,PRSS54,PTH1R,SLC36A2,SLC6A18,SP7 | AK1,CAMK2B,CARM1,CCDC28B,CCR3,DVL1,DYRK1B, ENDOG,GAPDH,GLT1D1,IMPA2,INHBE,IPO13,KLHDC3, MACROD1,LINC00116,NDUFB10,PHOSPHO1,SHISA4,TPI1,UBAC1 | ||||
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| ABCB4,C11orf21,CST7,DMRT1,ELSPBP1,EMX2,EMX2OS, EPHX1,EYA1,FCRLB,FHOD3,GLP1R,HIGD1C,HRNR, KIAA0087,OR10H1,PHOSPHO1,PTP4A3,SLC30A2,SYN3,TSPAN32 | SLC35G3,ARG1,BEND2,LINC00305,CMTM2,CXCR1,CXCR2, FAM74A4,FCGR3B,GAGE10,LRIT1,NXF4,OR52E6,PADI4, PHOSPHO1,PLCZ1,SELE,SLC22A24,SPRR2G,STRA8,ZNF735 |
| 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 |
: Open all plots for all cancer types
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| Interacting Genes (from Pathway Commons) |
: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID
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| Pharmacological Information for PHOSPHO1 |
| 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. |
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| * Drug Centered Interaction Network. |
| DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
| DB00122 | phosphatase, orphan 1 | approved; nutraceutical | Choline |  |  |
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| Cross referenced IDs for PHOSPHO1 |
| * We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
: Open all cross reference information
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