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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CHST12 |
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Phenotypic Information for CHST12(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: CHST12 |
Familial Cancer Database: CHST12 |
* 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/ |
Metabolic Pathway Description | |
KEGG_SULFUR_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: CHST12 |
MedGen: CHST12 (Human Medical Genetics with Condition) | |
ClinVar: CHST12 | |
Phenotype | MGI: CHST12 (International Mouse Phenotyping Consortium) |
PhenomicDB: CHST12 |
Mutations for CHST12 |
* 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 CHST12 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 |
CF127449 | COL3A1 | 1 | 486 | 2 | 189867773 | 189870167 | CHST12 | 485 | 782 | 7 | 2472625 | 2472922 |
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 |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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=29) | (# total SNVs=13) |
(# 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 |
chr7:2473276-2473276 | p.I334I | 4 |
chr7:2472309-2472309 | p.V12G | 3 |
chr7:2473018-2473018 | p.F248F | 3 |
chr7:2472823-2472823 | p.I183I | 2 |
chr7:2473033-2473033 | p.S253S | 2 |
chr7:2472296-2472296 | p.R8W | 2 |
chr7:2472883-2472883 | p.P203P | 2 |
chr7:2472376-2472376 | p.F34F | 2 |
chr7:2473211-2473211 | p.E313K | 1 |
chr7:2472615-2472615 | p.S114I | 1 |
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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 | 2 | 1 |   | 9 |   |   | 2 |   | 1 |   |   | 6 | 2 |   |   |   | 10 | 8 |   | 4 |
# mutation | 2 | 1 |   | 9 |   |   | 2 |   | 1 |   |   | 5 | 2 |   |   |   | 11 | 9 |   | 4 |
nonsynonymous SNV | 1 |   |   | 5 |   |   | 2 |   | 1 |   |   | 5 | 1 |   |   |   | 4 | 6 |   | 3 |
synonymous SNV | 1 | 1 |   | 4 |   |   |   |   |   |   |   |   | 1 |   |   |   | 7 | 3 |   | 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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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 |
chr7:2472309 | p.I334I,CHST12 | 3 |
chr7:2473276 | p.V12G,CHST12 | 3 |
chr7:2472883 | p.P52P,CHST12 | 2 |
chr7:2472430 | p.P203P,CHST12 | 2 |
chr7:2472864 | p.I22I,CHST12 | 1 |
chr7:2473129 | p.R197H,CHST12 | 1 |
chr7:2472524 | p.D348D,CHST12 | 1 |
chr7:2472865 | p.A31T,CHST12 | 1 |
chr7:2472296 | p.R197R,CHST12 | 1 |
chr7:2473134 | p.Q361H,CHST12 | 1 |
Other DBs for Point Mutations |
Copy Number for CHST12 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 CHST12 |
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 |
ADAT3,BRAT1,C7orf50,CCM2,CHST12,CYBA,ABHD17A, FASTK,AP5Z1,LYL1,MAD1L1,MGAT1,PRKCDBP,RHOG, RNF166,SIPA1,SLC39A13,TMUB1,TNFRSF4,TRADD,TWF2 | A4GALT,ARHGDIA,CHST12,EGLN2,GIMAP1,GUK1,HLX, JOSD2,LMF2,LRP3,MAP3K11,METRNL,NUCB1,PKN1, PLOD3,POLD4,PRKCDBP,RABAC1,RNH1,SLC9A3R2,TSPAN4 |
CCDC102A,CHST12,CLEC11A,EVA1B,FAM20C,GNA12,HIC1, HLX,HOMER3,KANK3,LPPR2,PLD3,RAB3IL1,SHANK3, SIPA1,SLC12A4,SLC39A13,SOX18,TGFB1,TSPAN4,UBTD1 | B3GALT6,CBX4,CCDC85B,CCR10,CHST12,DNASE2,ERCC2, EVA1B,H1FX,HIC1,HOMER3,LRFN1,MOSPD3,PLD3, PLEKHM2,RNF166,SIPA1,TGFB1,USP20,XAB2,ZNF777 |
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 CHST12 |
There's no related Drug. |
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Cross referenced IDs for CHST12 |
* 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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