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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for FXN |
Basic gene info. | Gene symbol | FXN |
Gene name | frataxin | |
Synonyms | CyaY|FA|FARR|FRDA|X25 | |
Cytomap | UCSC genome browser: 9q21.11 | |
Genomic location | chr9 :71650478-71693993 | |
Type of gene | protein-coding | |
RefGenes | NM_000144.4, NM_001161706.1,NM_181425.2, | |
Ensembl id | ENSG00000165060 | |
Description | Friedreich ataxia proteinfrataxin, mitochondrial | |
Modification date | 20141222 | |
dbXrefs | MIM : 606829 | |
HGNC : HGNC | ||
Ensembl : ENSG00000165060 | ||
HPRD : 06013 | ||
Protein | UniProt: Q16595 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_FXN | |
BioGPS: 2395 | ||
Gene Expression Atlas: ENSG00000165060 | ||
The Human Protein Atlas: ENSG00000165060 | ||
Pathway | NCI Pathway Interaction Database: FXN | |
KEGG: FXN | ||
REACTOME: FXN | ||
ConsensusPathDB | ||
Pathway Commons: FXN | ||
Metabolism | MetaCyc: FXN | |
HUMANCyc: FXN | ||
Regulation | Ensembl's Regulation: ENSG00000165060 | |
miRBase: chr9 :71,650,478-71,693,993 | ||
TargetScan: NM_000144 | ||
cisRED: ENSG00000165060 | ||
Context | iHOP: FXN | |
cancer metabolism search in PubMed: FXN | ||
UCL Cancer Institute: FXN | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for FXN(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: FXN |
Familial Cancer Database: FXN |
* 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 | |
REACTOME_METABOLISM_OF_PROTEINS |
Others | |
OMIM | 229300; phenotype. 606829; gene. |
Orphanet | 95; Friedreich ataxia. |
Disease | KEGG Disease: FXN |
MedGen: FXN (Human Medical Genetics with Condition) | |
ClinVar: FXN | |
Phenotype | MGI: FXN (International Mouse Phenotyping Consortium) |
PhenomicDB: FXN |
Mutations for FXN |
* 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 |
There's no intra-chromosomal structural variation. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | FXN | chr9 | 71674555 | 71674575 | ZNF673 | chr23 | 46311230 | 46311250 |
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 FXN 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 |
BM790417 | FXN | 1 | 386 | 9 | 71691342 | 71691727 | FXN | 380 | 680 | 9 | 71688985 | 71689282 | |
BF752849 | SNX22 | 5 | 93 | 15 | 64448234 | 64448323 | FXN | 77 | 102 | 9 | 71679533 | 71679561 |
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 |   |   |   |   |   |   | 12 |   |   |   |   |   |   |   | 1 |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   | 12 |   |   |   |   |   |   |   | 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=8) | (# total SNVs=3) |
(# 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 |
chr9:71687670-71687670 | p.D209H | 2 |
chr9:71679915-71679915 | p.T149M | 1 |
chr9:71679928-71679928 | p.Q153Q | 1 |
chr9:71679951-71679951 | p.S161I | 1 |
chr9:71687531-71687531 | p.G162G | 1 |
chr9:71687587-71687587 | p.S181F | 1 |
chr9:71687595-71687595 | p.E184* | 1 |
chr9:71668065-71668065 | p.D91D | 1 |
chr9:71668080-71668080 | p.E96E | 1 |
chr9:71668112-71668112 | p.A107V | 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 |   |   |   | 3 |   |   |   |   |   |   |   | 4 | 1 |   |   |   | 1 |   |   | 3 |
# mutation |   |   |   | 3 |   |   |   |   |   |   |   | 4 | 1 |   |   |   | 1 |   |   | 3 |
nonsynonymous SNV |   |   |   | 3 |   |   |   |   |   |   |   | 4 | 1 |   |   |   |   |   |   | 3 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 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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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 |
chr9:71687670 | p.D209H | 2 |
chr9:71679861 | p.D165G | 1 |
chr9:71679915 | p.V180M | 1 |
chr9:71679951 | p.V73D,FXN | 1 |
chr9:71687531 | p.G85C,FXN | 1 |
chr9:71687583 | p.D91D,FXN | 1 |
chr9:71661353 | p.A107V,FXN | 1 |
chr9:71661388 | p.F109L,FXN | 1 |
chr9:71668065 | p.V131A,FXN | 1 |
chr9:71668112 | p.T149M,FXN | 1 |
Other DBs for Point Mutations |
Copy Number for FXN 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 FXN |
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 |
ARL9,C9orf40,C9orf85,CDCA3,CKS2,FAM136A,FXN, LYAR,MRPL50,MRPS9,NDUFAF4,NOP2,NOP58,PDSS1, PSMG1,RPS7,SF3B14,SNRPD1,TEX10,TOMM5,UQCRH | AKAP6,BZW2,FAM210A,FAM220A,CISD1,DDN,DPF3, FHL3,FXN,HRASLS,HYAL4,IDI2,KCNQ5,MYLK4, NRG4,PPP2R3A,PRKCQ,SLC25A12,TMEM182,UTP11L,MSS51 |
ANP32B,BOLA3,CEP78,CHAC2,CKS2,COQ3,EXOSC2, FXN,HNRNPC,IARS,MMACHC,MRPL16,MRPL50,MRPS16, MRPS2,MTFMT,PA2G4,PMPCA,TEX10,TRIAP1,TRUB2 | ABCE1,BCCIP,BRIX1,CIRH1A,EI24,EIF3J,FASTKD2, FXN,MINA,NOC3L,PDCD2L,PMS1,PTMA,RCL1, RPP40,SMYD5,SRFBP1,TEX10,TIMM44,TTC4,WDR77 |
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 FXN |
There's no related Drug. |
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Cross referenced IDs for FXN |
* 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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