TissGDB

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	TissGeneSummary
	TissGeneExp
	TissGene-miRNA
	TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions
	TissGeneNet
	TissGeneProg
	TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for RFX2

Gene summary

Basic gene information	Gene symbol	RFX2
	Gene name
	Synonyms
	Cytomap	UCSC genome browser:
	Type of gene
	RefGenes
	Description
	Modification date
dbXrefs
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RFX2
	BioGPS: 101928900
Pathway	NCI Pathway Interaction Database: RFX2
	KEGG: RFX2
	REACTOME: RFX2
	Pathway Commons: RFX2
Context	iHOP: RFX2
	ligand binding site mutation search in PubMed: RFX2
	UCL Cancer Institute: RFX2
Assigned class in TissGDB*	C
Included tissue-specific gene expression resources	TiGER,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 annotations	Protective 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.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID

GO term

PubMed ID

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TissGeneExp for RFX2

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 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 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.

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)

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)

Cancer type	Mean(exp) in tumor	Mean(exp) in matched normal	Log2FC	P-val.	FDR
BRCA	0.08166694	1.664214309	-1.582547368	2.34E-28	2.79E-27
KICH	-1.275757937	0.200782063	-1.47654	6.51E-07	2.51E-06
LUSC	1.332742534	2.969271946	-1.636529412	4.93E-12	2.14E-11
KIRC	0.87743273	-0.201920048	1.079352778	4.85E-12	1.94E-11
LUAD	0.917835029	2.846364339	-1.92852931	1.11E-16	1.33E-15
ESCA	1.65393879	3.01953879	-1.3656	0.00119	0.016541
BLCA	1.194939747	2.601687116	-1.406747368	5.08E-05	0.000649306

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TissGene-miRNA for RFX2

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 type	miRNA id	miRNA accession	P-val.	Coeff.	# samples
ACC	hsa-miR-30e-5p	MIMAT0000692	0.02	-0.27	78
ACC	hsa-miR-30e-5p	MIMAT0000692	0.02	-0.27	78

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TissGeneMut for RFX2

TissGeneSNV for RFX2

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.

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)

- nsSNVs sorted by frequency.

AAchange	Cancer type	# samples
p.R169H	COAD	1
p.T254M	STAD	1
p.W202*	SKCM	1
p.P467S	SKCM	1
p.S621F	SKCM	1
p.R693H	BLCA	1
p.S219Y	STAD	1
p.N237S	COAD	1
p.E421K	HNSC	1
p.E706K	BLCA	1
p.R255W	DLBC	1
p.Q472R	PRAD	1
p.S219Y	READ	1
p.E96K	BLCA	1
p.W442*	BLCA	1
p.M157V	THYM	1
p.E671K	SKCM	1
p.M288V	UCEC	1
p.R291W	PAAD	1
p.G156V	BRCA	1
p.M177I	STAD	1
p.A12V	ACC	1
p.H599Y	THYM	1
p.T515M	PRAD	1
p.A473V	STAD	1
p.R280Q	DLBC	1
p.N487S	KICH	1
p.A600D	BRCA	1
p.R513H	STAD	1
p.L581V	ESCA	1
p.P63S	CESC	1
p.P128S	SKCM	1
p.K479*	HNSC	1
p.D700N	ESCA	1
p.A126V	HNSC	1
p.S219Y	UCEC	1
p.V564M	HNSC	1
p.M290I	KIRP	1
p.A239V	UCEC	1
p.W202X	SKCM	1
p.V72A	STAD	1
p.E211K	SKCM	1
p.V366I	HNSC	1
p.Y645H	SKCM	1
p.H639L	LUAD	1
p.D674N	UCEC	1
p.P603S	SKCM	1
p.S505N	SKCM	1
p.V549L	OV	1
p.S4Y	CESC	1
p.R566Q	STAD	1
p.T307M	ESCA	1
p.E421K	STAD	1
p.S621Y	ESCA	1
p.A423T	GBM	1
p.Q498L	STAD	1
p.R656H	PRAD	1
p.S142R	LUSC	1
p.R255W	SKCM	1
p.G636S	STAD	1
p.Q509R	STAD	1

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TissGeneCNV for RFX2

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)

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TissGeneFusions for RFX2

Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)

Database	Src	Cancer type	Sample	Fusion gene	ORF	5'-gene BP	3'-gene BP
Chimerdb3.0	ChiTaRs	NA	BF365469	RFX2-RFX2		chr19:6024327	chr19:6024313
Chimerdb3.0	ChiTaRs	NA	BF902834	RFX2-RFX2		chr19:6039842	chr19:6013055
Chimerdb3.0	FusionScan	ESCA	TCGA-Z6-A8JD-01A	RFX2-MLLT1	5'UTR-CDS	chr19:6110403	chr19:6230724
Chimerdb3.0	FusionScan	LUAD	TCGA-50-5946-01A	RFX2-EPOR	5'UTR-CDS	chr19:6110403	chr19:11489454
TCGAfusionPortal	PRADA	LUAD	TCGA-50-5946-01A	RFX2-EPOR	5UTR-CDS	Chr19:6110404	Chr19:11489454
TCGAfusionPortal	PRADA	LUAD	TCGA-78-7220-01A	RANBP3-RFX2	Out-of-frame	Chr19:5978072	Chr19:6016282

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TissGeneNet for RFX2

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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

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.

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.

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.

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.

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TissGeneClin for RFX2

TissGeneDrug for RFX2

Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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TissGeneDisease for RFX2

Disease information associated with TissGene
(DisGeNet, 2016-06-01)

Disease ID	Disease name	# pubmeds	Source
umls:C0004936	Mental disorders	1	GAD
umls:C0031511	Pheochromocytoma	1	BeFree