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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SMOX |
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Phenotypic Information for SMOX(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SMOX |
Familial Cancer Database: SMOX |
* 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_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_POLYAMINES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: SMOX |
MedGen: SMOX (Human Medical Genetics with Condition) | |
ClinVar: SMOX | |
Phenotype | MGI: SMOX (International Mouse Phenotyping Consortium) |
PhenomicDB: SMOX |
Mutations for SMOX |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SMOX 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 |
BF769727 | SMOX | 15 | 93 | 20 | 4167916 | 4167994 | SMOX | 90 | 253 | 20 | 4163469 | 4164277 | |
BC019054 | SMOX | 49 | 1509 | 20 | 4158151 | 4168367 | URM1 | 1510 | 2839 | 9 | 131133640 | 131153013 |
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 |   |   |   |   |   |   | 2 |   | 2 |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   | 1 |   | 2 |   |   |   |   |   |   |   |   |
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=52) | (# total SNVs=19) |
(# 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 |
chr20:4163144-4163144 | p.Q340* | 3 |
chr20:4164168-4164168 | p.R466Q | 2 |
chr20:4162483-4162483 | p.D157N | 2 |
chr20:4162485-4162485 | p.D157D | 2 |
chr20:4168011-4168011 | p.R542H | 2 |
chr20:4158083-4158083 | p.L98L | 2 |
chr20:4163401-4163401 | p.S425S | 2 |
chr20:4163028-4163028 | p.R301Q | 2 |
chr20:4162600-4162600 | p.A196S | 2 |
chr20:4155796-4155796 | p.A32T | 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 | 3 | 1 | 1 | 10 | 1 |   |   |   | 3 |   |   | 6 | 4 |   |   |   | 7 | 5 |   | 17 |
# mutation | 3 | 1 | 1 | 9 | 1 |   |   |   | 3 |   |   | 6 | 4 |   |   |   | 7 | 5 |   | 20 |
nonsynonymous SNV | 3 |   |   | 4 | 1 |   |   |   | 2 |   |   | 4 | 4 |   |   |   | 4 | 5 |   | 17 |
synonymous SNV |   | 1 | 1 | 5 |   |   |   |   | 1 |   |   | 2 |   |   |   |   | 3 |   |   | 3 |
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 |
chr20:4162483 | p.D157N,SMOX | 3 |
chr20:4163401 | p.R179H,SMOX | 2 |
chr20:4162550 | p.R466Q,SMOX | 2 |
chr20:4164168 | p.S425S,SMOX | 2 |
chr20:4163035 | p.R177L,SMOX | 1 |
chr20:4168031 | p.S312P,SMOX | 1 |
chr20:4155822 | p.L452L,SMOX | 1 |
chr20:4163291 | p.R179C,SMOX | 1 |
chr20:4162601 | p.S312S,SMOX | 1 |
chr20:4164184 | p.P459H,SMOX | 1 |
Other DBs for Point Mutations |
Copy Number for SMOX 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 SMOX |
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 |
BCL11A,SMCO4,CEBPB,DPYS,DUOXA2,UBALD2,FCN3, ITIH4,KCNG2,KIFC3,MT1F,MT1L,MT1X,MT2A, NRTN,POLR2F,SLC7A5,SMOX,TGFA,TRMU,TSPO | AHCY,AP1M2,ARRDC1,ASTN2,ATP13A1,BATF,HID1, EMC10,DAK,ECE2,FAM83F,CAMSAP3,MARCKSL1,NIPSNAP1, PICK1,PYCR1,SMOX,SMPDL3B,ST14,STAP2,TRPM4 | ||||
ANKEF1,AP5S1,CDS2,CENPB,CSNK2A1,DDRGK1,FAM110A, NSFL1C,PANK2,PSMF1,PTPRA,RBCK1,RRBP1,SMOX, STK35,TASP1,TBC1D20,TRMT6,UBOX5,VPS16,ZCCHC3 | CDH5,COL18A1,DOC2B,ENG,GREB1,HSPA12B,CEMIP, KRT7,LRRC37A3,MFRP,MMP2,MMRN2,PCDHGA12,PECAM1, PLXND1,POLR3H,RGS12,SMOX,SRPX2,TIE1,ZAR1L |
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 SMOX |
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 |
DB00127 | spermine oxidase | approved; nutraceutical | Spermine |
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Cross referenced IDs for SMOX |
* 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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