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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SMS |
Basic gene info. | Gene symbol | SMS |
Gene name | spermine synthase | |
Synonyms | MRSR|SPMSY|SRS|SpS | |
Cytomap | UCSC genome browser: Xp22.1 | |
Genomic location | chrX :21958714-22012955 | |
Type of gene | protein-coding | |
RefGenes | NM_001258423.1, NM_004595.4, | |
Ensembl id | ENSG00000102172 | |
Description | spermidine aminopropyltransferase | |
Modification date | 20141219 | |
dbXrefs | MIM : 300105 | |
HGNC : HGNC | ||
Ensembl : ENSG00000102172 | ||
HPRD : 02115 | ||
Vega : OTTHUMG00000021239 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SMS | |
BioGPS: 6611 | ||
Gene Expression Atlas: ENSG00000102172 | ||
The Human Protein Atlas: ENSG00000102172 | ||
Pathway | NCI Pathway Interaction Database: SMS | |
KEGG: SMS | ||
REACTOME: SMS | ||
ConsensusPathDB | ||
Pathway Commons: SMS | ||
Metabolism | MetaCyc: SMS | |
HUMANCyc: SMS | ||
Regulation | Ensembl's Regulation: ENSG00000102172 | |
miRBase: chrX :21,958,714-22,012,955 | ||
TargetScan: NM_001258423 | ||
cisRED: ENSG00000102172 | ||
Context | iHOP: SMS | |
cancer metabolism search in PubMed: SMS | ||
UCL Cancer Institute: SMS | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for SMS(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SMS |
Familial Cancer Database: SMS |
* 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/ |
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KEGG_CYSTEINE_AND_METHIONINE_METABOLISM KEGG_ARGININE_AND_PROLINE_METABOLISM KEGG_BETA_ALANINE_METABOLISM KEGG_GLUTATHIONE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_POLYAMINES |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: SMS |
MedGen: SMS (Human Medical Genetics with Condition) | |
ClinVar: SMS | |
Phenotype | MGI: SMS (International Mouse Phenotyping Consortium) |
PhenomicDB: SMS |
Mutations for SMS |
* 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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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SMS 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 |
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There's no copy number variation information in COSMIC data for this gene. |
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Stat. for Non-Synonymous SNVs (# total SNVs=25) | (# total SNVs=8) |
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(# total SNVs=2) | (# 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 |
chr23:21995314-21995314 | p.S155S | 2 |
chr23:21985352-21985352 | p.F30V | 2 |
chr23:22012446-22012446 | p.V360F | 1 |
chr23:21995254-21995254 | p.D135E | 1 |
chr23:21996172-21996172 | p.G200G | 1 |
chr23:21990083-21990083 | p.A80V | 1 |
chr23:22003297-22003298 | p.S302fs*27 | 1 |
chr23:21995260-21995260 | p.D137D | 1 |
chr23:21996176-21996176 | p.G202R | 1 |
chr23:21990627-21990627 | p.I89M | 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 |   |   |   | 5 | 1 |   | 2 |   | 1 |   |   | 2 | 4 | 1 |   |   | 3 | 3 |   | 10 |
# mutation |   |   |   | 5 | 1 |   | 2 |   | 1 |   |   | 2 | 4 | 1 |   |   | 4 | 4 |   | 11 |
nonsynonymous SNV |   |   |   | 4 |   |   | 2 |   | 1 |   |   | 2 | 4 |   |   |   | 1 | 2 |   | 7 |
synonymous SNV |   |   |   | 1 | 1 |   |   |   |   |   |   |   |   | 1 |   |   | 3 | 2 |   | 4 |
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 |
chrX:21995314 | p.S102S,SMS | 2 |
chrX:21995350 | p.D84D,SMS | 1 |
chrX:22010739 | p.C265Y,SMS | 1 |
chrX:21995187 | p.K98N,SMS | 1 |
chrX:21996172 | p.A271S,SMS | 1 |
chrX:22010804 | p.S102L,SMS | 1 |
chrX:21995200 | p.I292I,SMS | 1 |
chrX:21996187 | p.C294C,SMS | 1 |
chrX:22010810 | p.V295V,SMS | 1 |
chrX:21995222 | p.D18N,SMS | 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 SMS |
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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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APOO,ATP5C1,HGH1,C8orf76,COPS5,DCAF13,ENY2, MRPL15,MTERF3,NSMCE2,PDHA1,PIR,POLR2K,PRDX4, SMS,SNRPA1,TCEB1,TMEM70,TUBA1C,UBE2V2,ZNF706 | ATP6AP1,ATP6V1G1,COPZ1,CRABP2,DCAF13,DIABLO,H2AFY, HSBP1,ILF2,OCIAD2,PCNA,PDCL3,PPIA,RGS10, RPL39L,SEPHS2,SF3B14,SMS,SNRPF,TMEM199,VPS25 | ||||
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AIFM1,APEX2,APOO,CETN2,EMD,ERCC6L,FAM104B, FTSJ1,HCCS,HDAC8,HPRT1,NDUFB11,NKRF,PDK3, PDZD11,PIGA,PRPS2,RBBP7,SMS,SUV39H1,TSR2 | BCCIP,C19orf53,COPS3,DRG1,ENOPH1,ERH,FBXO22, GLO1,METTL5,MORF4L2,N6AMT2,NANP,NUP54,PARK7, PEX3,PRTFDC1,PUS3,SMS,SNRPE,THOC7,TRIAP1 |
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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 SMS |
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DB Category | DB Name | DB's ID and Url link |
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* 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 |
DB00127 | spermine synthase | approved; nutraceutical | Spermine | ![]() | ![]() |
DB00134 | spermine synthase | approved; nutraceutical | L-Methionine | ![]() | ![]() |
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Cross referenced IDs for SMS |
* 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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