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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for IVD |
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Phenotypic Information for IVD(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: IVD |
Familial Cancer Database: IVD |
* 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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REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: IVD |
MedGen: IVD (Human Medical Genetics with Condition) | |
ClinVar: IVD | |
Phenotype | MGI: IVD (International Mouse Phenotyping Consortium) |
PhenomicDB: IVD |
Mutations for IVD |
* 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 IVD 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 |
AA232469 | IVD | 1 | 86 | 15 | 40703459 | 40703544 | IVD | 81 | 197 | 15 | 40702909 | 40703487 | |
BM797058 | IVD | 1 | 103 | 15 | 40711358 | 40711460 | PTGES | 99 | 434 | 9 | 132500840 | 132501175 | |
AI928420 | IVD | 1 | 375 | 15 | 40713130 | 40713505 | MALAT1 | 372 | 456 | 11 | 65267923 | 65268007 | |
AA618569 | IVD | 1 | 374 | 15 | 40713130 | 40713505 | MALAT1 | 371 | 523 | 11 | 65267855 | 65268007 |
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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=27) | (# total SNVs=5) |
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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 |
chr15:40699846-40699846 | p.T55A | 5 |
chr15:40707606-40707606 | p.M298I | 2 |
chr15:40710373-40710373 | p.R398* | 2 |
chr15:40702862-40702862 | p.H111Y | 2 |
chr15:40710412-40710412 | p.E411K | 2 |
chr15:40702940-40702940 | p.I137V | 2 |
chr15:40707160-40707160 | p.V289G | 2 |
chr15:40699897-40699897 | p.D72N | 1 |
chr15:40703778-40703778 | p.N195S | 1 |
chr15:40707610-40707610 | p.A300T | 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 |   |   | 5 |   |   | 1 |   | 1 |   |   | 5 | 2 | 2 |   | 1 | 3 | 7 |   | 2 |
# mutation | 1 |   |   | 2 |   |   | 1 |   | 1 |   |   | 5 | 2 | 2 |   | 1 | 4 | 8 |   | 2 |
nonsynonymous SNV | 1 |   |   | 2 |   |   | 1 |   | 1 |   |   | 4 |   | 2 |   | 1 | 2 | 4 |   | 1 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   | 1 | 2 |   |   |   | 2 | 4 |   | 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 |
chr15:40699846 | p.T55A | 5 |
chr15:40710403 | p.K78K | 1 |
chr15:40700156 | p.A270V,IVD | 1 |
chr15:40705252 | p.G58R,IVD | 1 |
chr15:40710429 | p.M295V,IVD | 1 |
chr15:40702870 | p.L83L,IVD | 1 |
chr15:40705279 | p.A308T,IVD | 1 |
chr15:40702942 | p.I107I,IVD | 1 |
chr15:40707145 | p.E322G,IVD | 1 |
chr15:40702993 | p.P124P,IVD | 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 IVD |
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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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ARFIP2,BBS4,FAM174B,RMDN3,FOXA1,IVD,KIAA0319L, LCMT2,MFAP1,MOAP1,MPI,FAN1,NDUFAF1,P4HTM, PNPLA4,SPG11,SUOX,TADA2B,TMEM25,TTC8,VPS39 | AACS,ACSL3,ADAM2,B3GAT1,DHCR7,DHRS2,FDFT1, GGT1,HIST1H4H,HPGD,IDI1,IVD,LONP2,MPV17L, MVK,PNLIPRP3,PPEF1,SERHL2,SERHL,SULT1C3,UGT2B28 | ||||
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AQR,BAHD1,HYPK,CDAN1,EIF2AK4,RMDN3,FAM98B, GALK2,INO80,IVD,LOC729082,MPI,PAK6,PDIA3, PDIA3P1,PPIP5K1,RPAP1,RPUSD2,RTF1,SFXN2,SPATA5L1 | BEND3,C19orf57,EPHB2,FKTN,FOXA1,IVD,LIMD1, LRPPRC,MLEC,MRPS25,PLAGL1,PPM1H,PROM2,RPS10P7, SLC12A2,SUPV3L1,TARS2,TAS1R3,TP53,TRPM5,VGLL4 |
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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 IVD |
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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 |
DB03147 | isovaleryl-CoA dehydrogenase | experimental | Flavin-Adenine Dinucleotide | ![]() | ![]() |
DB04036 | isovaleryl-CoA dehydrogenase | experimental | Coenzyme a Persulfide | ![]() | ![]() |
DB00121 | isovaleryl-CoA dehydrogenase | approved; nutraceutical | Biotin | ![]() | ![]() |
DB00149 | isovaleryl-CoA dehydrogenase | approved; nutraceutical | L-Leucine | ![]() | ![]() |
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Cross referenced IDs for IVD |
* 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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