|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| |
| Phenotypic Information (metabolism pathway, cancer, disease, phenome) |
| |
| |
| Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG |
| |
|
| Gene Summary for HAGH |
| Top |
| Phenotypic Information for HAGH(metabolism pathway, cancer, disease, phenome) |
 Cancer Description | |
| Cancer | CGAP: HAGH |
| Familial Cancer Database: HAGH | |
| * 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_PYRUVATE_METABOLISM | |
| Others | |
| OMIM | |
| Orphanet | |
| Disease | KEGG Disease: HAGH |
| MedGen: HAGH (Human Medical Genetics with Condition) | |
| ClinVar: HAGH | |
| Phenotype | MGI: HAGH (International Mouse Phenotyping Consortium) |
| PhenomicDB: HAGH | |
| Mutations for HAGH |
| * 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 HAGH 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 |
| Other DBs for Structural Variants |
| Top |
| 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) |
| Top |
| SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
: Non-synonymous mutation, 
: Synonymous mutation, Circle size denotes number of samples. |
| Top |
| Somatic Mutation Counts per Tissue in COSMIC data |
| Stat. for Non-Synonymous SNVs (# total SNVs=12) | (# total SNVs=8) |
 |  |
(# total SNVs=1) | (# total SNVs=1) |
 |  |
| Top |
| 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 |
| chr16:1866933-1866933 | p.P188P | 3 |
| chr16:1867224-1867224 | p.A149V | 2 |
| chr16:1872330-1872330 | p.L47L | 2 |
| chr16:1872925-1872925 | p.L16V | 2 |
| chr16:1867182-1867182 | p.L163P | 1 |
| chr16:1869999-1869999 | p.N63D | 1 |
| chr16:1867196-1867196 | p.E158D | 1 |
| chr16:1870002-1870002 | p.G62R | 1 |
| chr16:1859305-1859305 | p.Q254H | 1 |
| chr16:1867243-1867243 | p.K143E | 1 |
| Top |
| SNV Counts per Each Loci in TCGA data |
|
 |
| 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 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 2 | 4 | 1 | ||||||||
| # mutation | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 2 | 4 | 1 | ||||||||
| nonsynonymous SNV | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 3 | ||||||||||||
| synonymous SNV | 1 | 1 | 1 | 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]) |
| Top |
| 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 |
| chr16:1866933 | p.P200L | 3 |
| chr16:1872925 | p.L64V,HAGH | 2 |
| chr16:1869197 | p.T97P,HAGH | 1 |
| chr16:1869933 | p.L64L,HAGH | 1 |
| chr16:1869958 | p.R297C,HAGH | 1 |
| chr16:1859322 | p.R294L,HAGH | 1 |
| chr16:1869997 | p.P271S,HAGH | 1 |
| chr16:1859330 | p.N238D,HAGH | 1 |
| chr16:1872326 | p.R170M,HAGH | 1 |
| chr16:1859771 | p.R161W,HAGH | 1 |
| Other DBs for Point Mutations |
| Copy Number for HAGH 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] |
| Top |
| Gene Expression for HAGH |
| 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)) |
 |
| Top |
| CNV vs Gene Expression Plot |
| * This plots show the correlation between CNV and gene expression. |
: Open all plots for all cancer types
 |
|
 |
|
| Top |
| 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 |
: Open all plots for all cancer types
 |
| ||||
| AMDHD2,TSR3,CCDC78,FAM173A,FAM195A,FBXL15,HAGHL, METRN,MPG,MRPL28,MRPS34,NARFL,NDUFB10,NME3, NUBP2,PGP,POLR2L,RHOT2,SCAND1,STUB1,TMEM191A | ADCK5,B4GALNT4,C16orf59,CLN6,DCTPP1,FBXL6,FEN1, GALE,SLC52A2,HAGHL,MAZ,METRN,PAFAH1B3,PAQR4, PUS1,PYCRL,RECQL4,RHPN1,RNASEH2A,TPRN,TRIM11 | ||||
 |
| ||||
| ATP5D,ADM5,CCDC78,CSN3,CT47A1,DCDC1,DPP7, F12,FAM173A,FBXL16,FSCN2,HAGHL,ITGA2B,KCNK7, KLRC1,KREMEN2,METRN,MT1H,OR6V1,SSPO,STUB1 | APBA3,APOBEC3D,C19orf60,PPP1R35,DNAJC4,ABHD17A,FBXL15, HAGHL,INO80B,LIME1,LRRC26,MUTYH,OGFOD2,PLCB2, RGS14,SIPA1,TRADD,TSSK6,USF2,ZNF524,ZNF837 |
| 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 |
: Open all plots for all cancer types
| Top |
| Interacting Genes (from Pathway Commons) |
: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID
| Top |
| Pharmacological Information for HAGH |
| 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 |
| DB00143 | hydroxyacylglutathione hydrolase | approved; nutraceutical | Glutathione |  |  |
| DB03889 | hydroxyacylglutathione hydrolase | experimental | S-(N-Hydroxy-N-Bromophenylcarbamoyl)Glutathione |  |  |
| Top |
| Cross referenced IDs for HAGH |
| * We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
: Open all cross reference information
|
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |