TissGDB

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

TissGeneSummary for CSTA

Gene summary

Basic gene information	Gene symbol	CSTA
	Gene name	cystatin A (stefin A)
	Synonyms	AREI\|STF1\|STFA
	Cytomap	UCSC genome browser: 3q21
	Type of gene	protein-coding
	RefGenes	NM_005213.3,
	Description	cystatin AScystatin-A
	Modification date	20141207
dbXrefs	MIM : 184600
	HGNC : HGNC
	Ensembl : ENSG00000121552
	HPRD : 01697
	Vega : OTTHUMG00000159488
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CSTA
	BioGPS: 1475
Pathway	NCI Pathway Interaction Database: CSTA
	KEGG: CSTA
	REACTOME: CSTA
	Pathway Commons: CSTA
Context	iHOP: CSTA
	ligand binding site mutation search in PubMed: CSTA
	UCL Cancer Institute: CSTA
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)	EsophagusProstate
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)	ESCAPRAD
Reference showing the relevant tissue of CSTA
Description by TissGene annotations

* 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:0010466	negative regulation of peptidase activity	6203523
GO:0010951	negative regulation of endopeptidase activity	3488317
GO:0018149	peptide cross-linking	10908733
GO:0030216	keratinocyte differentiation	10908733
GO:0045861	negative regulation of proteolysis	3488317
GO:0010466	negative regulation of peptidase activity	6203523
GO:0010951	negative regulation of endopeptidase activity	3488317
GO:0018149	peptide cross-linking	10908733
GO:0030216	keratinocyte differentiation	10908733
GO:0045861	negative regulation of proteolysis	3488317

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TissGeneExp for CSTA

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
LUAD	0.031393043	1.391843043	-1.36045	1.21E-11	8.35E-11
KIRP	-1.69109909	-3.757208465	2.066109375	1.18E-07	7.02E-07
KIRC	-0.861486937	-3.573979993	2.712493056	3.13E-28	5.12E-27
LUSC	3.696108324	1.431378912	2.264729412	1.59E-07	4.35E-07
BRCA	-0.425016908	0.863972566	-1.288989474	8.64E-12	3.67E-11
PRAD	-0.879174331	0.580898746	-1.460073077	1.77E-08	2.07E-07
HNSC	5.276294006	6.861540517	-1.585246512	0.00799	0.020405789

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TissGene-miRNA for CSTA

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

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TissGeneMut for CSTA

TissGeneSNV for CSTA

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.G36E	SKCM	2
p.V69I	LUAD	1
p.K91N	DLBC	1
p.G75R	GBM	1
p.F70L	READ	1
p.E15D	SKCM	1
p.R58Q	SKCM	1
p.L27P	SKCM	1
p.G97V	SARC	1
p.M65T	COAD	1
p.L38F	LUAD	1
p.D21N	BLCA	1

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TissGeneCNV for CSTA

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 CSTA

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	BE840750	EPC2-CSTA		chr2:149528956	chr3:122044130
Chimerdb3.0	ChiTaRs	NA	BE716971	CSTA-EPC2		chr3:122060458	chr2:149528937
Chimerdb3.0	ChiTaRs	NA	AW265472	CSTA-CSTA		chr3:122060376	chr3:122044154
Chimerdb3.0	ChiTaRs	NA	BE840752	MDGA2-CSTA		chr14:47730706	chr3:122044117
Chimerdb3.0	ChiTaRs	NA	BE840739	MRPS35-CSTA		chr12:27909002	chr3:122060371
Chimerdb3.0	TopHat-Fusion	PRAD	TCGA-G9-A9S4-01A	FAM162A-CSTA	CDS-5'UTR	chr3:122103145	chr3:122044107
Chimerdb3.0	TopHat-Fusion	PRAD	TCGA-G9-A9S4-01A	FAM162A-CSTA	Out-of-Frame	chr3:122103145	chr3:122056393
Chimerdb3.0	TopHat-Fusion	LUSC	TCGA-92-8065-01A	CSTA-CASR	In-Frame	chr3:122056494	chr3:121994658
TCGAfusionPortal	PRADA	KIRC	TCGA-BP-4774-01A	INPP5A-CSTA	In-frame	Chr10:134563349	Chr3:122056394

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TissGeneNet for CSTA

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)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

COAD (tumor)	COAD (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

HNSC (tumor)	HNSC (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

KICH (tumor)	KICH (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

KIRC (tumor)	KIRC (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

KIRP (tumor)	KIRP (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

LIHC (tumor)	LIHC (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

LUAD (tumor)	LUAD (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

LUSC (tumor)	LUSC (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

PRAD (tumor)	PRAD (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

STAD (tumor)	STAD (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

THCA (tumor)	THCA (normal)
CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (tumor)	CSTA, CUL2, UBC, PTN, KIAA0101, CUL4B, IVL, CTSL1, TCF3, CTSB, KRT1, RAD21, UCHL5, DSP, LOR, EVPL, USP53, TFAP2C, PI3, CTSH (normal)

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TissGeneProg for CSTA

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 CSTA

TissGeneDrug for CSTA

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 CSTA

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

Disease ID	Disease name	# pubmeds	Source
umls:C0376358	Malignant neoplasm of prostate	4	BeFree
umls:C0600139	Prostate carcinoma	4	BeFree
umls:C0027627	Neoplasm Metastasis	3	BeFree,CTD_human,LHGDN
umls:C0033860	Psoriasis	3	BeFree,GAD,LHGDN
umls:C0006142	Malignant neoplasm of breast	2	BeFree
umls:C0011849	Diabetes Mellitus	2	BeFree
umls:C0020757	Ichthyoses	2	BeFree
umls:C0020758	Congenital ichthyosis	2	BeFree
umls:C0178874	Tumor Progression	2	BeFree
umls:C0242656	Disease Progression	2	CTD_human
umls:C0678222	Breast Carcinoma	2	BeFree
umls:C0001418	Adenocarcinoma	1	BeFree
umls:C0004096	Asthma	1	BeFree
umls:C0006118	Brain Neoplasms	1	BeFree
umls:C0007131	Non-Small Cell Lung Carcinoma	1	BeFree
umls:C0007137	Squamous cell carcinoma	1	BeFree
umls:C0011615	Dermatitis, Atopic	1	BeFree,LHGDN
umls:C0011847	Diabetes	1	BeFree
umls:C0013595	Eczema	1	BeFree
umls:C0017601	Glaucoma	1	BeFree
umls:C0017636	Glioblastoma	1	CTD_human
umls:C0024117	Chronic Obstructive Airway Disease	1	BeFree
umls:C0025202	melanoma	1	BeFree
umls:C0042344	Varicose Ulcer	1	BeFree
umls:C0153676	Secondary malignant neoplasm of lung	1	BeFree
umls:C0153690	Secondary malignant neoplasm of bone	1	BeFree
umls:C0242379	Malignant neoplasm of lung	1	BeFree
umls:C0279626	Squamous cell carcinoma of esophagus	1	BeFree
umls:C0684249	Carcinoma of lung	1	BeFree
umls:C0853879	Invasive breast carcinoma	1	BeFree
umls:C1134719	Invasive Ductal Breast Carcinoma	1	BeFree
umls:C1168401	Squamous cell carcinoma of the head and neck	1	BeFree
umls:C1334015	High Grade Intraepithelial Neoplasia	1	BeFree
umls:C1458155	Mammary Neoplasms	1	LHGDN
umls:C2931822	Nasopharyngeal carcinoma	1	BeFree,CTD_human
umls:C1842797	Exfoliative Ichthyosis, Autosomal Recessive, Ichthyosis Bullosa of Siemens-like	0	CLINVAR,ORPHANET