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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TDO2 |
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Phenotypic Information for TDO2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: TDO2 |
Familial Cancer Database: TDO2 |
* 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/ |
Metabolic Pathway Description | |
KEGG_TRYPTOPHAN_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: TDO2 |
MedGen: TDO2 (Human Medical Genetics with Condition) | |
ClinVar: TDO2 | |
Phenotype | MGI: TDO2 (International Mouse Phenotyping Consortium) |
PhenomicDB: TDO2 |
Mutations for TDO2 |
* 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 TDO2 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 |
BG314637 | TDO2 | 3 | 77 | 4 | 156828925 | 156830093 | GZMB | 73 | 448 | 14 | 25101153 | 25102198 |
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 |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |
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=50) | (# total SNVs=6) |
(# total SNVs=0) | (# 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 |
chr4:156835532-156835532 | p.E262K | 2 |
chr4:156831336-156831336 | p.Q197H | 2 |
chr4:156831247-156831247 | p.L168I | 2 |
chr4:156832694-156832694 | p.F222V | 2 |
chr4:156831270-156831270 | p.Y175Y | 2 |
chr4:156826238-156826238 | p.A54V | 1 |
chr4:156838607-156838607 | p.S319S | 1 |
chr4:156830159-156830159 | p.D142Y | 1 |
chr4:156841045-156841045 | p.R375Q | 1 |
chr4:156825180-156825180 | p.K16* | 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 |   | 12 | 1 |   | 2 |   |   |   |   | 5 | 2 |   |   | 1 | 5 | 7 | 1 | 4 |
# mutation | 2 | 1 |   | 13 | 1 |   | 2 |   |   |   |   | 4 | 2 |   |   | 1 | 6 | 7 | 1 | 5 |
nonsynonymous SNV | 2 | 1 |   | 11 |   |   | 1 |   |   |   |   | 4 | 2 |   |   | 1 | 5 | 5 | 1 | 3 |
synonymous SNV |   |   |   | 2 | 1 |   | 1 |   |   |   |   |   |   |   |   |   | 1 | 2 |   | 2 |
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 |
chr4:156831336 | p.Q197H | 2 |
chr4:156831237 | p.K164N | 2 |
chr4:156828925 | p.S319L | 1 |
chr4:156841122 | p.L18L | 1 |
chr4:156825188 | p.R172T | 1 |
chr4:156838606 | p.M331R | 1 |
chr4:156830041 | p.K27N | 1 |
chr4:156831349 | p.R178I | 1 |
chr4:156825215 | p.G337D | 1 |
chr4:156839316 | p.T30A | 1 |
Other DBs for Point Mutations |
Copy Number for TDO2 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 TDO2 |
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 |
BMP1,CCDC102B,COL5A3,COL6A1,COL6A2,DAZL,EGFL6, EMILIN1,FOLR2,LEPRE1,LOC284688,MMP13,MMP9,OLFML2B, PCOLCE,RDH8,RFX8,S100A3,TBX2,TDO2,THY1 | ADSL,AGMAT,BZW2,CCDC28B,COL19A1,E2F8,ESRRB, FAM78A,GAPDH,HPCAL4,KCNN2,MAST2,NOTUM,P2RX5, PADI2,RBM20,SEMA4D,SH2B2,TDO2,TRIM69,TUBA4A | ||||
ANO8,ANP32A-IT1,C3orf22,CNKSR2,COL20A1,DEPDC7,DNAJB8, HEATR4,LOC285045,LOC729799,LRRC10,LTB4R,LTB4R2,SCNN1D, TDO2,TRIM49,TRIM77,TYK2,ZMAT4,ZSCAN9,ZSCAN23 | C4BPB,CD1B,CD80,CLEC4A,CXCL1,DNAJB11,FPR1, LILRA5,LLPH,LOC653566,MANF,MMP12,NAMPT,PSMC2, SDF2L1,SEC11C,SEC61B,SPCS2,SRGN,TDO2,TNFRSF6B |
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 TDO2 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00130 | tryptophan 2,3-dioxygenase | approved; nutraceutical; investigational | L-Glutamine | ||
DB00160 | tryptophan 2,3-dioxygenase | approved; nutraceutical | L-Alanine | ||
DB00150 | tryptophan 2,3-dioxygenase | approved; nutraceutical | L-Tryptophan |
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Cross referenced IDs for TDO2 |
* 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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