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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CHAT |
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Phenotypic Information for CHAT(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: CHAT |
Familial Cancer Database: CHAT |
* 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_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: CHAT |
MedGen: CHAT (Human Medical Genetics with Condition) | |
ClinVar: CHAT | |
Phenotype | MGI: CHAT (International Mouse Phenotyping Consortium) |
PhenomicDB: CHAT |
Mutations for CHAT |
* 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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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
breast | CHAT | chr10 | 50841766 | 50841766 | CHAT | chr10 | 50850501 | 50850501 |
ovary | CHAT | chr10 | 50841487 | 50841507 | CHAT | chr10 | 50843737 | 50843757 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CHAT 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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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   | 1 |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   | 1 |   |   |   |   | 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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Stat. for Non-Synonymous SNVs (# total SNVs=81) | (# total SNVs=42) |
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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 |
chr10:50835688-50835688 | p.R323H | 5 |
chr10:50873054-50873054 | p.E737K | 3 |
chr10:50856579-50856579 | p.C436* | 3 |
chr10:50859978-50859978 | p.G520G | 3 |
chr10:50835781-50835781 | p.T354R | 3 |
chr10:50870760-50870760 | p.E637K | 2 |
chr10:50856565-50856565 | p.R432R | 2 |
chr10:50856570-50856570 | p.D433E | 2 |
chr10:50835719-50835719 | p.L333L | 2 |
chr10:50822376-50822376 | p.D47E | 2 |
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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 | 2 |   | 22 | 4 |   | 5 |   | 3 |   |   | 16 | 13 | 1 |   | 3 | 18 | 9 | 1 | 7 |
# mutation | 5 | 2 |   | 23 | 4 |   | 5 |   | 3 |   |   | 16 | 13 | 1 |   | 3 | 19 | 10 | 1 | 11 |
nonsynonymous SNV | 2 | 1 |   | 15 | 4 |   | 5 |   | 2 |   |   | 10 | 8 |   |   | 2 | 11 | 4 |   | 4 |
synonymous SNV | 3 | 1 |   | 8 |   |   |   |   | 1 |   |   | 6 | 5 | 1 |   | 1 | 8 | 6 | 1 | 7 |
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 |
chr10:50859978 | p.R205H,CHAT | 3 |
chr10:50835688 | p.G402G,CHAT | 3 |
chr10:50856565 | p.A439V,CHAT | 2 |
chr10:50833529 | p.R314R,CHAT | 2 |
chr10:50863176 | p.S8S,CHAT | 2 |
chr10:50824639 | p.P137S,CHAT | 2 |
chr10:50872873 | p.V251V,CHAT | 1 |
chr10:50822282 | p.D328N,CHAT | 1 |
chr10:50835666 | p.Q409Q,CHAT | 1 |
chr10:50857591 | p.A513P,CHAT | 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 CHAT |
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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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C6orf132,CHAT,CLASP1,CT45A5,CTAG1B,LOC148824,NIFK, MRPS10,MSGN1,NARF,NDRG1,NXF2,PIWIL1,PRSS33, RIOK1,SIX2,SLC18A3,TMEM117,TSN,USP25,XPO5 | NA,NA,NA,NA,NA,NA,NA, NA,NA,NA,NA,NA,NA,NA, NA,NA,NA,NA,NA,NA,NA | ||||
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ASTN1,ATCAY,PIANP,CABP7,CHAT,CLVS2,DPYSL4, FAM196A,FUT9,HPCAL4,JPH4,KIAA1045,LRRC4B,RGAG4, SLC7A14,SSTR2,SYT4,SYT6,TCEAL5,TMEM59L,UNC80 | ACAN,AWAT2,BMX,C20orf141,NCOR1P1,CCDC129,CHAT, CLEC4G,GPX5,KPRP,LCE2C,LPA,MEPE,CHODL-AS1, OR2D2,PGLYRP3,POU2F3,SH2D7,SNORA79,TRIM6-TRIM34,ZSWIM2 |
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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 CHAT |
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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 |
DB00122 | choline O-acetyltransferase | approved; nutraceutical | Choline | ![]() | ![]() |
DB01156 | choline O-acetyltransferase | approved | Bupropion | ![]() | ![]() |
DB03128 | choline O-acetyltransferase | experimental | Acetylcholine | ![]() | ![]() |
DB00843 | choline O-acetyltransferase | approved | Donepezil | ![]() | ![]() |
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Cross referenced IDs for CHAT |
* 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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