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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for RFX2
check button Gene summary
Basic gene informationGene symbolRFX2
Gene nameregulatory factor X, 2 (influences HLA class II expression)
Synonyms-
CytomapUCSC genome browser: 19p13.3
Type of geneprotein-coding
RefGenesNM_000635.3,
NM_134433.2,
DescriptionDNA binding protein RFX2DNA-binding protein RFX2HLA class II regulatory factor RFX2regulatory factor X 2trans-acting regulatory factor 2
Modification date20141207
dbXrefs MIM : 142765
HGNC : HGNC
Ensembl : ENSG00000087903
HPRD : 00824
Vega : OTTHUMG00000180711
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RFX2
BioGPS: 5990
PathwayNCI Pathway Interaction Database: RFX2
KEGG: RFX2
REACTOME: RFX2
Pathway Commons: RFX2
ContextiHOP: RFX2
ligand binding site mutation search in PubMed: RFX2
UCL Cancer Institute: RFX2
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Bone marrowTestisThymus
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LAMLTGCTTHYM
Reference showing the relevant tissue of RFX2
Description by TissGene annotationsProtective TissGene in OS
Cancer gene
TissgsLTS
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID


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TissGeneExp for RFX2

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
BRCA0.081666941.664214309-1.5825473682.34E-282.79E-27
KICH-1.2757579370.200782063-1.476546.51E-072.51E-06
LUSC1.3327425342.969271946-1.6365294124.93E-122.14E-11
KIRC0.87743273-0.2019200481.0793527784.85E-121.94E-11
LUAD0.9178350292.846364339-1.928529311.11E-161.33E-15
ESCA1.653938793.01953879-1.36560.001190.016541
BLCA1.1949397472.601687116-1.4067473685.08E-050.000649306


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TissGene-miRNA for RFX2

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples
ACChsa-miR-30e-5pMIMAT00006920.02-0.2778
ACChsa-miR-30e-5pMIMAT00006920.02-0.2778


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TissGeneMut for RFX2
TissGeneSNV for RFX2

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.R169HCOAD1
p.T254MSTAD1
p.W202*SKCM1
p.P467SSKCM1
p.S621FSKCM1
p.R693HBLCA1
p.S219YSTAD1
p.N237SCOAD1
p.E421KHNSC1
p.E706KBLCA1
p.R255WDLBC1
p.Q472RPRAD1
p.S219YREAD1
p.E96KBLCA1
p.W442*BLCA1
p.M157VTHYM1
p.E671KSKCM1
p.M288VUCEC1
p.R291WPAAD1
p.G156VBRCA1
p.M177ISTAD1
p.A12VACC1
p.H599YTHYM1
p.T515MPRAD1
p.A473VSTAD1
p.R280QDLBC1
p.N487SKICH1
p.A600DBRCA1
p.R513HSTAD1
p.L581VESCA1
p.P63SCESC1
p.P128SSKCM1
p.K479*HNSC1
p.D700NESCA1
p.A126VHNSC1
p.S219YUCEC1
p.V564MHNSC1
p.M290IKIRP1
p.A239VUCEC1
p.W202XSKCM1
p.V72ASTAD1
p.E211KSKCM1
p.V366IHNSC1
p.Y645HSKCM1
p.H639LLUAD1
p.D674NUCEC1
p.P603SSKCM1
p.S505NSKCM1
p.V549LOV1
p.S4YCESC1
p.R566QSTAD1
p.T307MESCA1
p.E421KSTAD1
p.S621YESCA1
p.A423TGBM1
p.Q498LSTAD1
p.R656HPRAD1
p.S142RLUSC1
p.R255WSKCM1
p.G636SSTAD1
p.Q509RSTAD1


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TissGeneCNV for RFX2

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for RFX2

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNABF365469RFX2-RFX2chr19:6024327chr19:6024313
Chimerdb3.0ChiTaRsNABF902834RFX2-RFX2chr19:6039842chr19:6013055
Chimerdb3.0FusionScanESCATCGA-Z6-A8JD-01ARFX2-MLLT15'UTR-CDSchr19:6110403chr19:6230724
Chimerdb3.0FusionScanLUADTCGA-50-5946-01ARFX2-EPOR5'UTR-CDSchr19:6110403chr19:11489454
TCGAfusionPortalPRADALUADTCGA-50-5946-01ARFX2-EPOR5UTR-CDSChr19:6110404Chr19:11489454
TCGAfusionPortalPRADALUADTCGA-78-7220-01ARANBP3-RFX2Out-of-frameChr19:5978072Chr19:6016282


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TissGeneNet for RFX2

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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COAD (tumor)COAD (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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HNSC (tumor)HNSC (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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KICH (tumor)KICH (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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KIRC (tumor)KIRC (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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KIRP (tumor)KIRP (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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LIHC (tumor)LIHC (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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LUAD (tumor)LUAD (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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LUSC (tumor)LUSC (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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PRAD (tumor)PRAD (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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STAD (tumor)STAD (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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THCA (tumor)THCA (normal)
RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (tumor)RFX2, MDFI, HLA-DPA1, HLA-DQB1, RFX1, RFX6, HLA-DRA, IL5RA, RFX4 (normal)
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TissGeneProg for RFX2

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for RFX2
TissGeneDrug for RFX2

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for RFX2

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0004936Mental disorders1GAD
umls:C0031511Pheochromocytoma1BeFree