TissGDB

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

TissGeneSummary for RASGEF1B

Gene summary

Basic gene information	Gene symbol	RASGEF1B
	Gene name	RasGEF domain family, member 1B
	Synonyms	GPIG4
	Cytomap	UCSC genome browser: 4q21.21
	Type of gene	protein-coding
	RefGenes	NM_001300735.1, NM_001300736.1,NM_152545.2,
	Description	GPI gamma-4GPI-gamma 4ras-GEF domain-containing family member 1B
	Modification date	20141207
dbXrefs	MIM : 614532
	HGNC : HGNC
	Ensembl : ENSG00000138670
	HPRD : 17955
	Vega : OTTHUMG00000160890
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RASGEF1B
	BioGPS: 153020
Pathway	NCI Pathway Interaction Database: RASGEF1B
	KEGG: RASGEF1B
	REACTOME: RASGEF1B
	Pathway Commons: RASGEF1B
Context	iHOP: RASGEF1B
	ligand binding site mutation search in PubMed: RASGEF1B
	UCL Cancer Institute: RASGEF1B
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)	Lung
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)	LUAD,LUSC
Reference showing the relevant tissue of RASGEF1B
Description by TissGene annotations	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
GO:0032320	positive regulation of Ras GTPase activity	19645719
GO:0032320	positive regulation of Ras GTPase activity	19645719

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TissGeneExp for RASGEF1B

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
LIHC	0.480972094	2.708852094	-2.22788	3.25E-13	7.37E-12
BRCA	0.23676627	1.270720656	-1.033954386	8.84E-17	5.11E-16
LUSC	0.694295114	2.601879428	-1.907584314	2.72E-18	2.56E-17
LUAD	1.027927129	2.44131506	-1.413387931	8.08E-21	1.85E-19
BLCA	-1.440317063	-0.325922327	-1.114394737	0.00439	0.024157241
KICH	-0.476265906	0.776778094	-1.253044	7.55E-05	0.000202436

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TissGene-miRNA for RASGEF1B

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
UVM	hsa-miR-30e-5p	MIMAT0000692	0.016	-0.27	80

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TissGeneMut for RASGEF1B

TissGeneSNV for RASGEF1B

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.H456Y	SKCM	1
p.V268F	THCA	1
p.I377S	KIRC	1
p.S463F	SARC	1
p.N298H	ACC	1
p.V187L	LUAD	1
p.Y246C	KIRC	1
p.G29E	KIRC	1
p.Q169*	HNSC	1
p.D55Y	GBM	1
p.R349Q	READ	1
p.R149K	SKCM	1
p.Y57N	HNSC	1
p.A210S	LUAD	1
p.V269F	THCA	1
p.R264H	KICH	1
p.A406T	HNSC	1
p.K162R	THCA	1
p.G354E	BLCA	1
p.R426G	READ	1
p.R183L	LUAD	1
p.E454K	SKCM	1
p.T148A	KIRP	1
p.R319L	LUSC	1
p.W414C	PRAD	1
p.L352I	UCEC	1
p.V83I	COAD	1
p.P6S	BLCA	1
p.S175C	BLCA	1
p.E453K	SKCM	1
p.I380T	KIRC	1
p.A209S	LUAD	1
p.E116K	SKCM	1
p.T208R	STAD	1
p.V397I	DLBC	1
p.K250N	READ	1
p.I381T	KIRC	1
p.R162H	READ	1
p.Q231X	ESCA	1
p.R150K	SKCM	1
p.Y266C	HNSC	1
p.V186L	LUAD	1
p.G353E	BLCA	1
p.R349Q	STAD	1
p.V472L	UCS	1
p.E259*	HNSC	1
p.R149G	HNSC	1
p.Q168*	HNSC	1
p.I194V	LGG	1
p.S244N	UCEC	1
p.E145K	UCEC	1
p.V327L	LUSC	1
p.A162S	KIRC	1
p.P6L	SKCM	1
p.H455Y	SKCM	1
p.R281Q	BLCA	1
p.N297H	ACC	1
p.M284I	BLCA	1

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TissGeneCNV for RASGEF1B

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 RASGEF1B

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	AK295616	ATP8A1-RASGEF1B		chr4:42659122	chr4:82348725
Chimerdb3.0	ChiTaRs	NA	BF845885	RASGEF1B-MTOR		chr4:82366349	chr1:11317791
Chimerdb3.0	ChiTaRs	NA	BF845891	RASGEF1B-MTOR		chr4:82366351	chr1:11317791
Chimerdb3.0	ChiTaRs	NA	BF845998	RASGEF1B-MTOR		chr4:82366349	chr1:11317826
Chimerdb3.0	ChiTaRs	NA	BI909609	RASGEF1B-LNPEP		chr4:82392035	chr5:96363436
TCGAfusionPortal	PRADA	PRAD	TCGA-KK-A6E1-01A	MNAT1-RASGEF1B	CDS-5UTR	Chr14:61201669	Chr4:82380668

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TissGeneNet for RASGEF1B

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)

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TissGeneProg for RASGEF1B

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 RASGEF1B

TissGeneDrug for RASGEF1B

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 RASGEF1B

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

Disease ID	Disease name	# pubmeds	Source
umls:C3495559	Juvenile arthritis	1	CTD_human