TissGDB

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

TissGeneSummary for CTH

Gene summary

Basic gene information	Gene symbol	CTH
	Gene name	cystathionine gamma-lyase
	Synonyms	-
	Cytomap	UCSC genome browser: 1p31.1
	Type of gene	protein-coding
	RefGenes	NM_001190463.1, NM_001902.5,NM_153742.4,
	Description	cystathionase (cystathionine gamma-lyase)cysteine desulfhydrasecysteine-protein sulfhydrasegamma-cystathionasehomoserine deaminasehomoserine dehydratase
	Modification date	20141222
dbXrefs	MIM : 607657
	HGNC : HGNC
	Ensembl : ENSG00000116761
	HPRD : 09633
	Vega : OTTHUMG00000009352
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CTH
	BioGPS: 1491
Pathway	NCI Pathway Interaction Database: CTH
	KEGG: CTH
	REACTOME: CTH
	Pathway Commons: CTH
Context	iHOP: CTH
	ligand binding site mutation search in PubMed: CTH
	UCL Cancer Institute: CTH
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)	Liver
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)	LIHC
Reference showing the relevant tissue of CTH
Description by TissGene annotations	Have significant anti-correlated miRNA

* 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:0018272	protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	19019829
GO:0019344	cysteine biosynthetic process	10212249
GO:0070814	hydrogen sulfide biosynthetic process	19019829
GO:0018272	protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	19019829
GO:0019344	cysteine biosynthetic process	10212249
GO:0070814	hydrogen sulfide biosynthetic process	19019829

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TissGeneExp for CTH

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	0.294492583	-0.781788452	1.076281034	1.73E-09	8.92E-09
KIRP	-0.09983565	1.34907685	-1.4489125	9.21E-08	5.58E-07
KIRC	-0.544269678	1.277112267	-1.821381944	2.60E-29	4.62E-28
LIHC	3.1568901	4.9816541	-1.824764	7.56E-07	4.17E-06
THCA	-0.797412239	0.962979286	-1.760391525	1.14E-18	3.24E-17
KICH	-0.2861599	1.0007961	-1.286956	0.000127	0.000323968

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TissGene-miRNA for CTH

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-27a-3p	MIMAT0000084	0.031	-0.29	56
UCS	hsa-miR-26b-5p	MIMAT0000083	0.022	-0.31	56
UCS	hsa-miR-30d-5p	MIMAT0000245	0.0095	-0.35	56
UCS	hsa-miR-30b-5p	MIMAT0000420	0.0007	-0.44	56

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TissGeneMut for CTH

TissGeneSNV for CTH

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.K131N	UCEC	2
p.W32*	STAD	1
p.E301*	UCEC	1
p.A6S	ESCA	1
p.E339D	HNSC	1
p.Y213*	BRCA	1
p.P66A	HNSC	1
p.E294K	BLCA	1
p.R205H	KIRC	1
p.G244V	BLCA	1
p.G212E	HNSC	1
p.E170*	BRCA	1
p.H324R	OV	1
p.E349Q	PCPG	1
p.T67A	UCEC	1
p.L390P	STAD	1
p.R375Q	STAD	1
p.Y60C	LIHC	1
p.G50W	LUAD	1
p.E157X	THYM	1
p.R343Q	STAD	1
p.P66S	SKCM	1
p.G280V	LUAD	1
p.R237H	KIRC	1
p.A325V	PRAD	1
p.C109Y	LGG	1
p.E30D	UCEC	1
p.E313K	READ	1
p.Q246E	BLCA	1
p.E351Q	BLCA	1
p.R205C	BLCA	1
p.R62L	GBM	1
p.Q306L	LIHC	1
p.Q278E	BLCA	1
p.G212V	BLCA	1
p.E307D	HNSC	1
p.A81T	COAD	1
p.S133Y	UCEC	1
p.E381Q	PCPG	1
p.R257*	BRCA	1
p.G50A	KIRP	1
p.I283L	COAD	1

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TissGeneCNV for CTH

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 CTH

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	H72721	CTH-CTH		chr1:70879919	chr1:70879222
Chimerdb3.0	ChiTaRs	NA	BX106222	CTH-CTH		chr1:70879836	chr1:70879812

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TissGeneNet for CTH

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)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

COAD (tumor)	COAD (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

HNSC (tumor)	HNSC (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

KICH (tumor)	KICH (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

KIRC (tumor)	KIRC (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

KIRP (tumor)	KIRP (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

LIHC (tumor)	LIHC (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

LUAD (tumor)	LUAD (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

LUSC (tumor)	LUSC (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

PRAD (tumor)	PRAD (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

STAD (tumor)	STAD (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

THCA (tumor)	THCA (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)	CTH, UBC, YWHAZ, SDCBP2 (normal)

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TissGeneProg for CTH

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 CTH

TissGeneDrug for CTH

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

DrugBank ID	Drug name	Drug activity	Drug type	Drug status
DB00151	L-Cysteine		Small molecule	Approved\|Nutraceutical

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TissGeneDisease for CTH

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

Disease ID	Disease name	# pubmeds	Source
umls:C0220993	Cystathioninuria	4	BeFree,CLINVAR,MGD,ORPHANET,UNIPROT
umls:C0268616	Gamma-cystathionase deficiency	3	BeFree,CTD_human,ORPHANET
umls:C0005684	Malignant neoplasm of urinary bladder	2	BeFree,GAD
umls:C0002986	Fabry Disease	1	BeFree
umls:C0004153	Atherosclerosis	1	GAD
umls:C0007102	Malignant tumor of colon	1	BeFree
umls:C0008924	Cleft Lip	1	GAD
umls:C0008925	Cleft Palate	1	GAD
umls:C0017636	Glioblastoma	1	BeFree
umls:C0020538	Hypertensive disease	1	BeFree
umls:C0021361	Female infertility	1	GAD
umls:C0021655	Insulin Resistance	1	GAD
umls:C0024117	Chronic Obstructive Airway Disease	1	GAD
umls:C0025202	melanoma	1	BeFree
umls:C0027819	Neuroblastoma	1	BeFree
umls:C0035235	Respiratory Syncytial Virus Infections	1	BeFree
umls:C0042373	Vascular Diseases	1	BeFree
umls:C0080178	Spina Bifida	1	GAD
umls:C0086543	Cataract	1	RGD
umls:C0242379	Malignant neoplasm of lung	1	GAD
umls:C0376358	Malignant neoplasm of prostate	1	BeFree
umls:C0600139	Prostate carcinoma	1	BeFree
umls:C0699790	Colon Carcinoma	1	BeFree
umls:C0699885	Carcinoma of bladder	1	BeFree
umls:C0700095	Central neuroblastoma	1	BeFree
umls:C0920646	Renal ischaemia	1	BeFree
umls:C2239176	Liver carcinoma	1	BeFree