TissGDB

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

TissGeneSummary for CLPB

Gene summary

Basic gene information	Gene symbol	CLPB
	Gene name	ClpB caseinolytic peptidase B homolog (E. coli)
	Synonyms	HSP78\|SKD3
	Cytomap	UCSC genome browser: 11q13.4
	Type of gene	protein-coding
	RefGenes	NM_001258392.1, NM_001258393.1,NM_001258394.1,NM_030813.4,
	Description	caseinolytic peptidase B protein homologsuppressor of potassium transport defect 3
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000162129
	HPRD : 11560
	Vega : OTTHUMG00000167902
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CLPB
	BioGPS: 81570
Pathway	NCI Pathway Interaction Database: CLPB
	KEGG: CLPB
	REACTOME: CLPB
	Pathway Commons: CLPB
Context	iHOP: CLPB
	ligand binding site mutation search in PubMed: CLPB
	UCL Cancer Institute: CLPB
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 CLPB
Description by TissGene annotations	Have significant anti-correlated miRNA TissgsLTS Fused withTSGene

* 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:0034605	cellular response to heat	2745427
GO:0034605	cellular response to heat	2745427

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TissGeneExp for CLPB

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
KICH	2.861069205	1.325213205	1.535856	4.01E-16	1.06E-14

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TissGene-miRNA for CLPB

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-339-5p	MIMAT0000764	0.024	-0.26	78
ACC	hsa-miR-339-5p	MIMAT0000764	0.024	-0.26	78
LUAD	hsa-let-7a-5p	MIMAT0000062	0.03	-0.28	60
LUAD	hsa-miR-22-3p	MIMAT0000077	0.025	-0.29	60
LUAD	hsa-let-7f-5p	MIMAT0000067	0.0099	-0.33	60

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TissGeneMut for CLPB

TissGeneSNV for CLPB

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.P92S	SKCM	2
p.R546C	SKCM	2
p.A306V	PRAD	1
p.K482N	CESC	1
p.E330*	SKCM	1
p.M298I	LUSC	1
p.N145D	UCEC	1
p.N448S	SARC	1
p.E636Q	READ	1
p.E297K	SKCM	1
p.R417*	HNSC	1
p.V274I	HNSC	1
p.A391V	SKCM	1
p.Y279C	BLCA	1
p.P243S	SKCM	1
p.R3C	LUAD	1
p.A306T	STAD	1
p.R334W	UCEC	1
p.G481R	STAD	1
p.V463M	KIRC	1
p.V160A	UCEC	1
p.R3C	BLCA	1
p.A459V	BLCA	1
p.A361V	SKCM	1
p.R3G	LUAD	1
p.V107I	PAAD	1
p.R674C	STAD	1
p.Q70*	BLCA	1
p.R516C	SKCM	1
p.T598M	UCEC	1
p.K702N	STAD	1
p.R297W	READ	1
p.P193R	LUSC	1
p.W168*	HNSC	1
p.D253Y	CESC	1
p.L166R	COAD	1
p.R417*	STAD	1
p.S59L	SKCM	1
p.I348V	LUAD	1
p.A522V	PRAD	1
p.E215K	SARC	1
p.F558I	SKCM	1
p.A513S	LUAD	1
p.R312Q	KICH	1
p.G3V	STAD	1
p.A306V	HNSC	1
p.R417Q	UCEC	1
p.R143H	PRAD	1
p.S663R	SARC	1
p.R73C	COAD	1
p.H164R	COAD	1
p.E575*	BLCA	1
p.P461S	SKCM	1
p.E267K	SKCM	1
p.D102V	KIRP	1
p.S155*	GBM	1
p.A51V	SKCM	1
p.R518C	UCEC	1
p.R3S	HNSC	1
p.S64F	SKCM	1
p.Y567C	CESC	1
p.A696V	HNSC	1
p.E435*	LUAD	1
p.P700A	SKCM	1
p.P431S	SKCM	1
p.P670A	SKCM	1

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TissGeneCNV for CLPB

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 CLPB

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	BX954309	CLPB-CABP4		chr11:72003817	chr11:67223119
Chimerdb3.0	ChiTaRs	NA	BF815616	CLPB-HECA		chr11:72053183	chr6:139499229
Chimerdb3.0	FusionScan	ESCA	TCGA-LN-A49W-01A	CLPB-GOLGA8B	CDS-5'UTR	chr11:72069923	chr15:34846157
Chimerdb3.0	FusionScan	ESCA	TCGA-LN-A49W-01A	CLPB-GOLGA8A	CDS-5'UTR	chr11:72069923	chr15:34699936
TCGAfusionPortal	PRADA	BRCA	TCGA-A8-A09D-01A	CLPB-ARMC4	In-frame	Chr11:72012847	Chr10:28229734
TCGAfusionPortal	PRADA	BRCA	TCGA-AR-A24K-01A	CLPB-MTUS2	In-frame	Chr11:72069924	Chr13:29674910
TCGAfusionPortal	PRADA	BRCA	TCGA-B6-A0RL-01A	CLPB-C2CD3	In-frame	Chr11:72040751	Chr11:73817538
TCGAfusionPortal	PRADA	BRCA	TCGA-BH-A0B9-01A	CLPB-STARD10	CDS-5UTR	Chr11:72091325	Chr11:72492339
TCGAfusionPortal	PRADA	HNSC	TCGA-CV-7418-01A	LRP5-CLPB	In-frame	Chr11:68080273	Chr11:72070052

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TissGeneNet for CLPB

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)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

COAD (tumor)	COAD (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

HNSC (tumor)	HNSC (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

KICH (tumor)	KICH (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

KIRC (tumor)	KIRC (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

KIRP (tumor)	KIRP (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

LIHC (tumor)	LIHC (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

LUAD (tumor)	LUAD (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

LUSC (tumor)	LUSC (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

PRAD (tumor)	PRAD (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

STAD (tumor)	STAD (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

THCA (tumor)	THCA (normal)
CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (tumor)	CLPB, SQSTM1, COPS6, HNF4A, MDFI, TERF2, CUL3, UCHL3, ATG2A, UVRAG, SMAD9, TTF2, USP30, OSBPL10 (normal)

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TissGeneProg for CLPB

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 CLPB

TissGeneDrug for CLPB

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 CLPB

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

Disease ID	Disease name	# pubmeds	Source
umls:C0342727	3-@METHYLGLUTACONIC ACIDURIA, TYPE I	2	BeFree
umls:C3696376	3-Methylglutaconic Aciduria	2	BeFree
umls:C0018203	Chronic granulomatous disease	1	BeFree
umls:C0085584	Encephalopathies	1	BeFree
umls:C0235820	Neonatal encephalopathy	1	BeFree
umls:C0235946	Cerebral atrophy	1	BeFree
umls:C0340970	Congenital neutropenia	1	BeFree
umls:C1853118	Severe congenital neutropenia	1	BeFree
umls:C3714756	Intellectual Disability	1	BeFree
umls:C3853041	Severe Congenital Microcephaly	1	BeFree