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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CKMT1B |
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Phenotypic Information for CKMT1B(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: CKMT1B |
Familial Cancer Database: CKMT1B |
* 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_ARGININE_AND_PROLINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: CKMT1B |
MedGen: CKMT1B (Human Medical Genetics with Condition) | |
ClinVar: CKMT1B | |
Phenotype | MGI: CKMT1B (International Mouse Phenotyping Consortium) |
PhenomicDB: CKMT1B |
Mutations for CKMT1B |
* 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 CKMT1B 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=7) | (# total SNVs=7) |
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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 |
chr15:43890515-43890515 | p.L334R | 1 |
chr15:43891426-43891426 | p.G403G | 1 |
chr15:43891069-43891069 | p.K352K | 1 |
chr15:43891435-43891435 | p.I406I | 1 |
chr15:43891071-43891071 | p.R353H | 1 |
chr15:43891083-43891083 | p.G357E | 1 |
chr15:43891099-43891099 | p.A362A | 1 |
chr15:43888609-43888609 | p.H252Q | 1 |
chr15:43891108-43891108 | p.G365G | 1 |
chr15:43888668-43888668 | p.S272F | 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 |   | 2 |   | 2 | 2 |   | 1 |   |   |   |   | 2 |   |   |   |   | 1 | 2 |   |   |
# mutation |   | 2 |   | 2 | 2 |   | 1 |   |   |   |   | 2 |   |   |   |   | 1 | 2 |   |   |
nonsynonymous SNV |   | 1 |   | 2 | 2 |   | 1 |   |   |   |   | 1 |   |   |   |   |   | 2 |   |   |
synonymous SNV |   | 1 |   |   |   |   |   |   |   |   |   | 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 |
chr15:43891383 | p.I406I | 1 |
chr15:43891392 | p.P411H | 1 |
chr15:43891410 | p.N319N | 1 |
chr15:43891425 | p.L320V | 1 |
chr15:43891435 | p.L334V | 1 |
chr15:43890471 | p.L334R | 1 |
chr15:43891449 | p.G357E | 1 |
chr15:43890472 | p.G365G | 1 |
chr15:43890514 | p.G389A | 1 |
chr15:43890515 | p.Y392C | 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 CKMT1B |
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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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AP3B2,APLP1,ASPHD1,ATP5B,KNSTRN,CDC25B,CHRNB2, CKMT1A,CKMT1B,CPLX2,ELL3,FAM155B,HCN2,KCNH2, LRTM2,PPFIA3,PPIP5K1,RELL2,TMEM151A,TMEM198,UNC13A | C19orf48,CKMT1B,DIRAS1,DTNB,EFNA4,ELMO3,IPO4, KCTD14,KRTCAP3,LAD1,POLR1C,PPAP2C,PRSS8,PVRL4, RAB25,RTKN,SAMD10,SH2D3A,SOX10,TMEM177,TP53 |
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ATP5B,ATP5D,TMEM253,C6orf136,CHCHD10,RHOV___CHP1,CKMT1A, CKMT1B,COX5A,ELL3,GALK2,GOT1,CLUH,MYO1A, NDUFS2,PPIP5K1,RDH13,S100A14,SCAMP2,SQRDL,UQCRC1 | ACSS2,AP1B1,CNOT11,CKMT1B,CSTF2,DLG3,DPP3, ELOVL1,FAR2,LGALS4,LOC407835,LYPLA2P1,MAP2K2,NDUFS2, NIPA2,PAPSS2,PKP3,PSMD3,TMEM53,TPRN,TTLL12 |
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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 CKMT1B |
There's no related Drug. |
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Cross referenced IDs for CKMT1B |
* 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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