TissGDB

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

TissGeneSummary for BRAP

Gene summary

Basic gene information	Gene symbol	BRAP
	Gene name	BRCA1 associated protein
	Synonyms	BRAP2\|IMP\|RNF52
	Cytomap	UCSC genome browser: 12q24
	Type of gene	protein-coding
	RefGenes	NM_006768.4,
	Description	BRCA1-associated proteinRING finger protein 52galectin-2-binding proteinimpedes mitogenic signal propagationrenal carcinoma antigen NY-REN-63
	Modification date	20141207
dbXrefs	MIM : 604986
	HGNC : HGNC
	Ensembl : ENSG00000089234
	Vega : OTTHUMG00000169600
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_BRAP
	BioGPS: 8315
Pathway	NCI Pathway Interaction Database: BRAP
	KEGG: BRAP
	REACTOME: BRAP
	Pathway Commons: BRAP
Context	iHOP: BRAP
	ligand binding site mutation search in PubMed: BRAP
	UCL Cancer Institute: BRAP
Assigned class in TissGDB*	C
Included tissue-specific gene expression resources	HPA,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)	Testis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)	TGCT
Reference showing the relevant tissue of BRAP
Description by TissGene annotations	Have significant anti-correlated miRNA 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:0000165	MAPK cascade	14724641
GO:0007265	Ras protein signal transduction	14724641
GO:0009968	negative regulation of signal transduction	14724641
GO:0016567	protein ubiquitination	14724641
GO:0000165	MAPK cascade	14724641
GO:0007265	Ras protein signal transduction	14724641
GO:0009968	negative regulation of signal transduction	14724641
GO:0016567	protein ubiquitination	14724641

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TissGeneExp for BRAP

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

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TissGene-miRNA for BRAP

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
UCS	hsa-miR-30d-5p	MIMAT0000245	0.028	-0.3	56
ACC	hsa-miR-340-5p	MIMAT0004692	0.00037	-0.4	78
ACC	hsa-miR-340-5p	MIMAT0004692	0.00037	-0.4	78

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TissGeneMut for BRAP

TissGeneSNV for BRAP

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.L416V	LIHC	2
p.E450D	LUSC	1
p.S289I	UCEC	1
p.R429W	READ	1
p.K246R	LGG	1
p.E392K	BLCA	1
p.L268M	THYM	1
p.E350K	BLCA	1
p.H139D	CESC	1
p.A565T	LIHC	1
p.R9P	BLCA	1
p.E34K	BRCA	1
p.P311L	LIHC	1
p.R209C	STAD	1
p.R376X	KIRP	1
p.T39M	STAD	1
p.Y356C	BLCA	1
p.P53S	SKCM	1
p.A251T	CESC	1
p.R376*	UCEC	1
p.P53L	SKCM	1
p.A481V	KICH	1
p.E186K	UCEC	1
p.R270C	DLBC	1
p.S468F	BLCA	1
p.C317Y	HNSC	1
p.E30D	UCEC	1
p.P53L	UCEC	1
p.R66S	ESCA	1
p.P199S	SKCM	1
p.S127L	SKCM	1
p.T281M	THCA	1
p.Q475*	BLCA	1
p.H106Y	LIHC	1
p.A214V	BLCA	1
p.L41V	LUAD	1
p.K444Q	COAD	1
p.V225E	PAAD	1
p.T265M	STAD	1
p.R67X	STAD	1
p.M219I	HNSC	1
p.R376*	KIRP	1
p.K85I	STAD	1
p.R420X	COAD	1
p.L455I	THYM	1
p.A58V	UCEC	1
p.F287L	CESC	1
p.T265A	LUAD	1
p.T448I	SKCM	1
p.T87I	SKCM	1
p.R67*	STAD	1
p.R554Q	SKCM	1
p.E417K	SKCM	1

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TissGeneCNV for BRAP

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 BRAP

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	DB055888	BRAP-CPT1B		chr12:112123760	chr22:51015874
TCGAfusionPortal	PRADA	LUSC	TCGA-18-4083-01A	BRAP-C12orf24	Out-of-frame	Chr12:112103443	Chr12:110927824

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TissGeneNet for BRAP

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)
BRAP, TRIM55, CUL2, HNF4A, BRCA1, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

COAD (tumor)	COAD (normal)
BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

HNSC (tumor)	HNSC (normal)
BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

KICH (tumor)	KICH (normal)
BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

KIRC (tumor)	KIRC (normal)
BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

KIRP (tumor)	KIRP (normal)
BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

LIHC (tumor)	LIHC (normal)
BRAP, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

LUAD (tumor)	LUAD (normal)
BRAP, TRIM55, CUL2, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TRIM8, CENPF, KSR1, LGALS2 (normal)

LUSC (tumor)	LUSC (normal)
BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

PRAD (tumor)	PRAD (normal)
BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

STAD (tumor)	STAD (normal)
BRAP, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

THCA (tumor)	THCA (normal)
BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, CNKSR1, MAP2K1, RAF1, TCF4, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (tumor)	BRAP, TRIM55, CUL2, HNF4A, BRCA1, UBC, HRAS, IKBKB, CNKSR1, MAP2K1, RAF1, BRAF, TRIM41, UBE2H, DDB1, CDC14A, TWIST1, TRIM8, CENPF, KSR1, LGALS2 (normal)

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TissGeneProg for BRAP

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 BRAP

TissGeneDrug for BRAP

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 BRAP

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

Disease ID	Disease name	# pubmeds	Source
umls:C0010054	Coronary Arteriosclerosis	3	BeFree
umls:C0027051	Myocardial Infarction	3	BeFree,CTD_human,GAD,GWASCAT
umls:C1956346	Coronary Artery Disease	3	BeFree
umls:C0004153	Atherosclerosis	2	BeFree,GAD
umls:C0010068	Coronary heart disease	2	BeFree
umls:C0023418	leukemia	2	BeFree
umls:C0524620	Metabolic Syndrome X	2	BeFree
umls:C0001973	Alcoholic Intoxication, Chronic	1	BeFree
umls:C0005586	Bipolar Disorder	1	BeFree
umls:C0006142	Malignant neoplasm of breast	1	BeFree
umls:C0007222	Cardiovascular Diseases	1	BeFree
umls:C0010418	Cryptosporidiosis	1	BeFree
umls:C0011860	Diabetes Mellitus, Non-Insulin-Dependent	1	BeFree
umls:C0017926	Glycogen Storage Disease Type VII	1	BeFree
umls:C0033817	Pseudomonas Infections	1	BeFree
umls:C0546837	Malignant neoplasm of esophagus	1	GAD
umls:C0549393	Alcohol problem	1	BeFree
umls:C0677886	Epithelial ovarian cancer	1	BeFree
umls:C0678222	Breast Carcinoma	1	BeFree