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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SDS |
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Phenotypic Information for SDS(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SDS |
Familial Cancer Database: SDS |
* 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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KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM KEGG_CYSTEINE_AND_METHIONINE_METABOLISM |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: SDS |
MedGen: SDS (Human Medical Genetics with Condition) | |
ClinVar: SDS | |
Phenotype | MGI: SDS (International Mouse Phenotyping Consortium) |
PhenomicDB: SDS |
Mutations for SDS |
* 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 SDS 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 |
AV645432 | SDS | 1 | 308 | 12 | 113830583 | 113830890 | GNA14 | 309 | 362 | 9 | 80136639 | 80136692 |
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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=21) | (# total SNVs=15) |
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(# total SNVs=1) | (# 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 |
chr12:113835134-113835134 | p.I163M | 5 |
chr12:113836602-113836602 | p.V81V | 3 |
chr12:113835004-113835004 | p.A207T | 2 |
chr12:113835050-113835050 | p.I191I | 2 |
chr12:113835119-113835119 | p.G168G | 2 |
chr12:113836935-113836935 | p.H59N | 2 |
chr12:113836325-113836325 | p.L140L | 1 |
chr12:113830787-113830817 | p.N307fs*6 | 1 |
chr12:113837402-113837402 | p.G38S | 1 |
chr12:113836340-113836340 | p.P135P | 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 | 1 |   |   | 4 | 1 |   |   |   |   |   |   | 5 | 4 |   |   |   | 3 | 2 |   | 6 |
# mutation | 1 |   |   | 3 | 1 |   |   |   |   |   |   | 5 | 4 |   |   |   | 3 | 2 |   | 5 |
nonsynonymous SNV | 1 |   |   | 3 |   |   |   |   |   |   |   | 3 | 2 |   |   |   |   | 2 |   | 1 |
synonymous SNV |   |   |   |   | 1 |   |   |   |   |   |   | 2 | 2 |   |   |   | 3 |   |   | 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 |
chr12:113835050 | p.I191I | 2 |
chr12:113835055 | p.V190I | 2 |
chr12:113837397 | p.A311T | 1 |
chr12:113830802 | p.A104V | 1 |
chr12:113835115 | p.E288K | 1 |
chr12:113837484 | p.K100Q | 1 |
chr12:113830871 | p.I264I | 1 |
chr12:113835119 | p.I85I | 1 |
chr12:113830941 | p.D261N | 1 |
chr12:113835157 | p.V81V | 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 SDS |
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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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APCS,APOA2,APOC2,APOC3,APOC4,ASGR2,C8A, C8G,C9,CATSPER1,CREB3L3,CRP,FABP1,HAMP, HP,ITIH1,MT1B,SDS,SERPINA7,SLC17A2,TM4SF5 | ADAM8,SOWAHD,APOC1,APOC2,ATP6V0D2,BCL2A1,CD300LF, CHIT1,DNAJC5B,HS3ST2,HTRA4,IL4I1,ITGAD,LILRA4, MEP1A,MMP9,PDE6G,PKD2L1,RAB42,SDS,SPATA12 | ||||
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C1QC,CD300A,CD68,CD86,CTSL,FCER1G,FCGR1A, FCGR1B,FPR3,GPNMB,HAVCR2,IFI30,LAPTM5,MS4A4A, MS4A7,MSR1,PLA2G7,RAB42,SDS,TREM2,TYROBP | ATP6V0D2,KIAA0226L,C21orf2,CLN8,CXXC1,DDA1,DLEC1, EMID1,ABHD17B,FAM160A2,FBXO34,FBXO46,NRG1,OVOL2, RCE1,ARHGAP44,RPL10L,SDS,TNS4,ZNF562,ZNF575 |
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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 SDS |
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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 |
DB00114 | serine dehydratase | nutraceutical | Pyridoxal Phosphate | ![]() | ![]() |
DB00133 | serine dehydratase | approved; nutraceutical | L-Serine | ![]() | ![]() |
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Cross referenced IDs for SDS |
* 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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