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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for CTH
check button Gene summary
Basic gene informationGene symbolCTH
Gene namecystathionine gamma-lyase
Synonyms-
CytomapUCSC genome browser: 1p31.1
Type of geneprotein-coding
RefGenesNM_001190463.1,
NM_001902.5,NM_153742.4,
Descriptioncystathionase (cystathionine gamma-lyase)cysteine desulfhydrasecysteine-protein sulfhydrasegamma-cystathionasehomoserine deaminasehomoserine dehydratase
Modification date20141222
dbXrefs MIM : 607657
HGNC : HGNC
Ensembl : ENSG00000116761
HPRD : 09633
Vega : OTTHUMG00000009352
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CTH
BioGPS: 1491
PathwayNCI Pathway Interaction Database: CTH
KEGG: CTH
REACTOME: CTH
Pathway Commons: CTH
ContextiHOP: CTH
ligand binding site mutation search in PubMed: CTH
UCL Cancer Institute: CTH
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,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 annotationsHave 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.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0018272protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine19019829
GO:0019344cysteine biosynthetic process10212249
GO:0070814hydrogen sulfide biosynthetic process19019829
GO:0018272protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine19019829
GO:0019344cysteine biosynthetic process10212249
GO:0070814hydrogen sulfide biosynthetic process19019829


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TissGeneExp for CTH

check button 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 exp


check button 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 isoform exp


check button 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.
normal gene exp


check button 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)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
LUAD0.294492583-0.7817884521.0762810341.73E-098.92E-09
KIRP-0.099835651.34907685-1.44891259.21E-085.58E-07
KIRC-0.5442696781.277112267-1.8213819442.60E-294.62E-28
LIHC3.15689014.9816541-1.8247647.56E-074.17E-06
THCA-0.7974122390.962979286-1.7603915251.14E-183.24E-17
KICH-0.28615991.0007961-1.2869560.0001270.000323968


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TissGene-miRNA for CTH

check button 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 typemiRNA idmiRNA accessionP-val.Coeff.# samples
UCShsa-miR-27a-3pMIMAT00000840.031-0.2956
UCShsa-miR-26b-5pMIMAT00000830.022-0.3156
UCShsa-miR-30d-5pMIMAT00002450.0095-0.3556
UCShsa-miR-30b-5pMIMAT00004200.0007-0.4456


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TissGeneMut for CTH
TissGeneSNV for CTH

check button 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.
SNV lollipop
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check button 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)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.K131NUCEC2
p.W32*STAD1
p.E301*UCEC1
p.A6SESCA1
p.E339DHNSC1
p.Y213*BRCA1
p.P66AHNSC1
p.E294KBLCA1
p.R205HKIRC1
p.G244VBLCA1
p.G212EHNSC1
p.E170*BRCA1
p.H324ROV1
p.E349QPCPG1
p.T67AUCEC1
p.L390PSTAD1
p.R375QSTAD1
p.Y60CLIHC1
p.G50WLUAD1
p.E157XTHYM1
p.R343QSTAD1
p.P66SSKCM1
p.G280VLUAD1
p.R237HKIRC1
p.A325VPRAD1
p.C109YLGG1
p.E30DUCEC1
p.E313KREAD1
p.Q246EBLCA1
p.E351QBLCA1
p.R205CBLCA1
p.R62LGBM1
p.Q306LLIHC1
p.Q278EBLCA1
p.G212VBLCA1
p.E307DHNSC1
p.A81TCOAD1
p.S133YUCEC1
p.E381QPCPG1
p.R257*BRCA1
p.G50AKIRP1
p.I283LCOAD1


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TissGeneCNV for CTH

check button 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)
CNV


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TissGeneFusions for CTH

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNAH72721CTH-CTHchr1:70879919chr1:70879222
Chimerdb3.0ChiTaRsNABX106222CTH-CTHchr1:70879836chr1:70879812


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TissGeneNet for CTH

check button 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)
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COAD (tumor)COAD (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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HNSC (tumor)HNSC (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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KICH (tumor)KICH (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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KIRC (tumor)KIRC (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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KIRP (tumor)KIRP (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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LIHC (tumor)LIHC (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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LUAD (tumor)LUAD (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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LUSC (tumor)LUSC (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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PRAD (tumor)PRAD (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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STAD (tumor)STAD (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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THCA (tumor)THCA (normal)
CTH, UBC, YWHAZ, SDCBP2 (tumor)CTH, UBC, YWHAZ, SDCBP2 (normal)
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TissGeneProg for CTH

check button 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.
survival 1

check button 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.
survival 2

check button 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.
survival 3

check button 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.
survival 4

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TissGeneClin for CTH
TissGeneDrug for CTH

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status
DB00151L-CysteineSmall moleculeApproved|Nutraceutical


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TissGeneDisease for CTH

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0220993Cystathioninuria4BeFree,CLINVAR,MGD,ORPHANET,UNIPROT
umls:C0268616Gamma-cystathionase deficiency3BeFree,CTD_human,ORPHANET
umls:C0005684Malignant neoplasm of urinary bladder2BeFree,GAD
umls:C0002986Fabry Disease1BeFree
umls:C0004153Atherosclerosis1GAD
umls:C0007102Malignant tumor of colon1BeFree
umls:C0008924Cleft Lip1GAD
umls:C0008925Cleft Palate1GAD
umls:C0017636Glioblastoma1BeFree
umls:C0020538Hypertensive disease1BeFree
umls:C0021361Female infertility1GAD
umls:C0021655Insulin Resistance1GAD
umls:C0024117Chronic Obstructive Airway Disease1GAD
umls:C0025202melanoma1BeFree
umls:C0027819Neuroblastoma1BeFree
umls:C0035235Respiratory Syncytial Virus Infections1BeFree
umls:C0042373Vascular Diseases1BeFree
umls:C0080178Spina Bifida1GAD
umls:C0086543Cataract1RGD
umls:C0242379Malignant neoplasm of lung1GAD
umls:C0376358Malignant neoplasm of prostate1BeFree
umls:C0600139Prostate carcinoma1BeFree
umls:C0699790Colon Carcinoma1BeFree
umls:C0699885Carcinoma of bladder1BeFree
umls:C0700095Central neuroblastoma1BeFree
umls:C0920646Renal ischaemia1BeFree
umls:C2239176Liver carcinoma1BeFree