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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SCO2 |
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Phenotypic Information for SCO2(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SCO2 |
Familial Cancer Database: SCO2 |
* 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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Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145 |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: SCO2 |
MedGen: SCO2 (Human Medical Genetics with Condition) | |
ClinVar: SCO2 | |
Phenotype | MGI: SCO2 (International Mouse Phenotyping Consortium) |
PhenomicDB: SCO2 |
Mutations for SCO2 |
* 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 SCO2 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=22) | (# total SNVs=3) |
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(# total SNVs=0) | (# 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 |
chr22:50962782-50962782 | p.R20P | 4 |
chr22:50962330-50962330 | p.R171W | 2 |
chr22:50962178-50962178 | p.I221I | 2 |
chr22:50962183-50962183 | p.Y220H | 2 |
chr22:50962224-50962224 | p.R206H | 2 |
chr22:50962057-50962057 | p.R262C | 1 |
chr22:50962076-50962076 | p.R255R | 1 |
chr22:50962398-50962398 | p.V148G | 1 |
chr22:50962077-50962077 | p.R255Q | 1 |
chr22:50962405-50962405 | p.Q146* | 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 |   | 1 |   |   | 3 |   |   | 1 |   | 2 |   |   |   |   |   | 1 |   | 2 |
# mutation |   | 1 |   | 1 |   |   | 7 |   |   | 1 |   | 2 |   |   |   |   |   | 1 |   | 2 |
nonsynonymous SNV |   |   |   | 1 |   |   | 5 |   |   | 1 |   | 2 |   |   |   |   |   |   |   | 1 |
synonymous SNV |   | 1 |   |   |   |   | 2 |   |   |   |   |   |   |   |   |   |   | 1 |   | 1 |
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 |
chr22:50962076 | p.R255R,SCO2 | 1 |
chr22:50962761 | p.D234N,SCO2 | 1 |
chr22:50962141 | p.H224R,SCO2 | 1 |
chr22:50962769 | p.I221I,SCO2 | 1 |
chr22:50962170 | p.Y180Y,SCO2 | 1 |
chr22:50962803 | p.V174I,SCO2 | 1 |
chr22:50962178 | p.R112R,SCO2 | 1 |
chr22:50962824 | p.E83D,SCO2 | 1 |
chr22:50962301 | p.E81K,SCO2 | 1 |
chr22:50962321 | p.E45K,SCO2 | 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 SCO2 |
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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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ALG12,ARSA,CHKB,CRELD2,GUK1,LMF2,NCAPH2, NOL12,ODF3B,PRR5,RPS19BP1,PPP6R2,SCO2,SELO, THAP7,TMUB1,TOM1,TRABD,TRMU,TSPO,TYMP | BAD,C19orf24,C9orf16,CFL1,COPE,DTYMK,MVB12A, FIBP,GNB2,MPG,PPP1CA,PPP4C,PTRH1,SCO2, SNAPC2,TBCB,TMEM208,TRAPPC5,YIF1A,YIF1B,ZDHHC12 |
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AKR1A1,PTRHD1,ECI1,EIF5A,EIF5AL1,NAA38,MCAT, MIF,MRPL27,MRPL43,MRPL54,NDUFA6,PSMA6,RBX1, RPS19BP1,SCO2,SF3B5,TOMM22,TSPO,TXN2,UQCRC1 | BOLA2,UQCC3,MIEN1,CCDC12,CHCHD1,DCTPP1,LOC729991, LSM4,LSM7,MRPL14,MRPL27,MRPL54,NDUFS3,OVCA2, PPP4C,ROMO1,SCO2,SF3B5,TMSB10,TSPO,UQCR10 |
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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 SCO2 |
There's no related Drug. |
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Cross referenced IDs for SCO2 |
* 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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