|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for NRF1 |
Top |
Phenotypic Information for NRF1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: NRF1 |
Familial Cancer Database: NRF1 |
* 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 | |
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: NRF1 |
MedGen: NRF1 (Human Medical Genetics with Condition) | |
ClinVar: NRF1 | |
Phenotype | MGI: NRF1 (International Mouse Phenotyping Consortium) |
PhenomicDB: NRF1 |
Mutations for NRF1 |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
prostate | NRF1 | chr7 | 129390737 | 129390737 | chr7 | 155389558 | 155389558 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NRF1 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 |
BC006380 | NRF1 | 21 | 409 | 7 | 129351313 | 129367207 | EIF4A1 | 407 | 1574 | 17 | 7478436 | 7482036 | |
AA503463 | NRF1 | 8 | 73 | 7 | 129377030 | 129377095 | NRF1 | 68 | 265 | 7 | 129376917 | 129377114 | |
CV341784 | UBE2D3 | 35 | 90 | 4 | 103717295 | 103717350 | NRF1 | 87 | 653 | 7 | 129269870 | 129270436 |
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 |   |   |   |   |   |   | 3 |   | 2 |   |   | 1 |   |   |   | |||
GAIN (# sample) | 1 | 1 |   |   |   |   |   |   | 3 |   | 2 |   |   | 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) |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=35) | (# total SNVs=13) |
(# total SNVs=1) | (# total SNVs=0) |
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 |
chr7:129297332-129297332 | p.S47S | 3 |
chr7:129357178-129357178 | p.E395E | 3 |
chr7:129317479-129317479 | p.R116* | 3 |
chr7:129317486-129317486 | p.T118M | 2 |
chr7:129357140-129357140 | p.A383T | 2 |
chr7:129367082-129367082 | p.E409K | 2 |
chr7:129351322-129351322 | p.T324M | 2 |
chr7:129367102-129367102 | p.V415V | 1 |
chr7:129395005-129395005 | p.V499A | 1 |
chr7:129349051-129349051 | p.R248L | 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 | 2 | 1 | 5 | 2 |   | 3 |   | 1 |   | 1 | 6 |   | 1 |   |   | 4 | 8 |   | 5 |
# mutation | 1 | 2 | 1 | 5 | 2 |   | 3 |   | 1 |   | 1 | 9 |   | 1 |   |   | 4 | 8 |   | 6 |
nonsynonymous SNV |   | 1 | 1 | 4 | 1 |   | 3 |   | 1 |   | 1 | 5 |   | 1 |   |   | 4 | 6 |   | 5 |
synonymous SNV | 1 | 1 |   | 1 | 1 |   |   |   |   |   |   | 4 |   |   |   |   |   | 2 |   | 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 |
chr7:129367082 | p.E248K,NRF1 | 3 |
chr7:129357144 | p.T118M,NRF1 | 2 |
chr7:129317486 | p.S223L,NRF1 | 2 |
chr7:129348982 | p.Y298Y,NRF1 | 1 |
chr7:129351329 | p.V24M,NRF1 | 1 |
chr7:129297261 | p.Q111L,NRF1 | 1 |
chr7:129394886 | p.A306T,NRF1 | 1 |
chr7:129348999 | p.T33T,NRF1 | 1 |
chr7:129351377 | p.R114L,NRF1 | 1 |
chr7:129297290 | p.G308S,NRF1 | 1 |
Other DBs for Point Mutations |
Copy Number for NRF1 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 NRF1 |
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. |
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 |
DDX39B,CLDN15,CROCCP2,DGCR8,EGFL8,GIGYF1,ING5, KRBA1,LOC390595,MAP2K7,NRF1,POLR2J4,PRKRIP1,SAFB, CLASRP,SFSWAP,WASH7P,WDR27,ZNF212,ZNF767P,ZNF862 | ACTR5,BRD1,BZRAP1,CHDH,DVL2,GEMIN4,HAUS5, LIMK2,NRF1,POLDIP3,RIPK4,SART3,SFSWAP,SH2D3A, UNK,WDR6,XPC,ZNF202,ZNF263,ZNF346,ZSCAN25 |
ASXL1,LINC01000,GIGYF1,GMEB2,ILF3,INE1,LOC100129637, LOC349114,LY6G5B,NRF1,PASK,PLCG1,RBM33,SFSWAP, SNORA71E,TJAP1,UCKL1-AS1,ZMIZ2,ZNF212,ZNF335,ZSCAN25 | ARFGAP2,CEP131,BAP1,CIZ1,DVL2,EHMT2,ERCC2, FKBP9,H1FX,IFT122,IFT140,KLHL26,MKL1,NRF1, PATZ1,PDE4A,PLEKHM2,SF3A2,UBE2O,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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for NRF1 |
There's no related Drug. |
Top |
Cross referenced IDs for NRF1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |