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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RFK |
Basic gene info. | Gene symbol | RFK |
Gene name | riboflavin kinase | |
Synonyms | RIFK | |
Cytomap | UCSC genome browser: 9q21.13 | |
Genomic location | chr9 :79000432-79009444 | |
Type of gene | protein-coding | |
RefGenes | NM_018339.5, | |
Ensembl id | ENSG00000135002 | |
Description | 0610038L10RikATP:riboflavin 5'-phosphotransferaseflavokinase | |
Modification date | 20141207 | |
dbXrefs | MIM : 613010 | |
HGNC : HGNC | ||
Ensembl : ENSG00000135002 | ||
HPRD : 17969 | ||
Vega : OTTHUMG00000020040 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RFK | |
BioGPS: 55312 | ||
Gene Expression Atlas: ENSG00000135002 | ||
The Human Protein Atlas: ENSG00000135002 | ||
Pathway | NCI Pathway Interaction Database: RFK | |
KEGG: RFK | ||
REACTOME: RFK | ||
ConsensusPathDB | ||
Pathway Commons: RFK | ||
Metabolism | MetaCyc: RFK | |
HUMANCyc: RFK | ||
Regulation | Ensembl's Regulation: ENSG00000135002 | |
miRBase: chr9 :79,000,432-79,009,444 | ||
TargetScan: NM_018339 | ||
cisRED: ENSG00000135002 | ||
Context | iHOP: RFK | |
cancer metabolism search in PubMed: RFK | ||
UCL Cancer Institute: RFK | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RFK(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: RFK |
Familial Cancer Database: RFK |
* 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_RIBOFLAVIN_METABOLISM REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: RFK |
MedGen: RFK (Human Medical Genetics with Condition) | |
ClinVar: RFK | |
Phenotype | MGI: RFK (International Mouse Phenotyping Consortium) |
PhenomicDB: RFK |
Mutations for RFK |
* 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 RFK 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 |
BC015473 | RFK | 1 | 1046 | 9 | 79001916 | 79009266 | LYZ | 1047 | 1534 | 12 | 69747527 | 69748014 | |
Z25253 | SGCD | 2 | 68 | 5 | 155771567 | 155771633 | RFK | 58 | 261 | 9 | 79000724 | 79000926 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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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=11) | (# total SNVs=0) |
(# total SNVs=2) | (# total SNVs=1) |
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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 |
chr9:79002369-79002369 | p.I145M | 3 |
chr9:79007414-79007415 | p.S59fs*8 | 2 |
chr9:79002433-79002433 | p.S124L | 1 |
chr9:79002440-79002440 | p.L122F | 1 |
chr9:79003486-79003486 | p.K114N | 1 |
chr9:79003508-79003508 | p.V107A | 1 |
chr9:79002337-79002337 | p.S156N | 1 |
chr9:79002362-79002362 | p.D148N | 1 |
chr9:79007422-79007422 | p.G56A | 1 |
chr9:79002365-79002366 | p.E147fs*9 | 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 | 1 | 1 |   | 1 |   |   |   |   |   |   |   |   |   |   |   | 1 |   | 1 |   | 1 |
# mutation | 1 | 1 |   | 1 |   |   |   |   |   |   |   |   |   |   |   | 1 |   | 1 |   | 1 |
nonsynonymous SNV | 1 | 1 |   | 1 |   |   |   |   |   |   |   |   |   |   |   | 1 |   | 1 |   | 1 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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 |
chr9:79002362 | p.D141N | 1 |
chr9:79002415 | p.I123T | 1 |
chr9:79002418 | p.D122V | 1 |
chr9:79003486 | p.K107N | 1 |
chr9:79003508 | p.V100A | 1 |
chr9:79009015 | p.I25V | 1 |
Other DBs for Point Mutations |
Copy Number for RFK 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 RFK |
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 |
BSPH1,C2orf69,LINC00588,C9orf41,ISCA1,ISCA1P1,LEUTX, PRAMEF5,PRAMEF9,RAB14,RBM18,RFK,RFPL4B,PTBP3, SCAMP1,SIM1,SPRR3,SPTLC1,TPRX1,TRIM53AP,UBQLN1 | ABHD13,TMEM263,MZT1,C1D,CHMP2B,COMMD8,EIF4E, FAM3C,IMPA1,MOB4,MOSPD1,RFK,SELT,SMNDC1, SPCS3,TRAM1,TXNDC9,UBE2D3,UBE2E1,UBLCP1,ZCCHC10 | ||||
ARL5A,ATP6V1G1,C12orf29,C1D,TRAPPC13,COMMD8,ISCA1, ISCA1P1,MOB4,PDCD10,RARS2,RFK,RNASEH2B,RSL24D1, SLC35D2,SPTLC1,SRP9,TGDS,TXNDC9,YWHAQ,ZCCHC10 | ARPC5,ABRACL,CASP7,CHMP2B,GDPD3,GHITM,GNG12, GRAMD3,HPGD,LRRC19,MIER1,MYL12B,NAT1,SLC51B, RAC1,RFK,SPPL2A,SRI,TPMT,UBE2A,WSB2 |
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 RFK |
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 |
DB00140 | riboflavin kinase | approved; nutraceutical | Riboflavin | ||
DB03247 | riboflavin kinase | experimental | Riboflavin Monophosphate | ||
DB03431 | riboflavin kinase | experimental | Adenosine-5'-Diphosphate |
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Cross referenced IDs for RFK |
* 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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