TissGDB

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

TissGeneSummary for ARX

Gene summary

Basic gene information	Gene symbol	ARX
	Gene name	aristaless related homeobox
	Synonyms	CT121\|EIEE1\|ISSX\|MRX29\|MRX32\|MRX33\|MRX36\|MRX38\|MRX43\|MRX54\|MRX76\|MRX87\|MRXS1\|PRTS
	Cytomap	UCSC genome browser: Xp21.3
	Type of gene	protein-coding
	RefGenes	NM_139058.2,
	Description	aristaless-related homeobox, X-linkedcancer/testis antigen 121homeobox protein ARX
	Modification date	20141207
dbXrefs	MIM : 300382
	HGNC : HGNC
	Ensembl : ENSG00000004848
	HPRD : 02307
	Vega : OTTHUMG00000021275
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ARX
	BioGPS: 170302
Pathway	NCI Pathway Interaction Database: ARX
	KEGG: ARX
	REACTOME: ARX
	Pathway Commons: ARX
Context	iHOP: ARX
	ligand binding site mutation search in PubMed: ARX
	UCL Cancer Institute: ARX
Assigned class in TissGDB*	B
Included tissue-specific gene expression resources	HPA,TiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)	OvaryPancreas
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)	OVPAAD
Reference showing the relevant tissue of ARX
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

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TissGeneExp for ARX

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
COAD	-0.803853028	0.475196972	-1.27905	0.00652	0.015100761
PRAD	2.894081588	1.782629665	1.111451923	0.00334	0.009161493
LUSC	-0.651516753	0.470751874	-1.122268627	0.00484	0.008128024

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TissGene-miRNA for ARX

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
LUAD	hsa-miR-27a-3p	MIMAT0000084	0.038	-0.27	60
UCS	hsa-miR-130a-3p	MIMAT0000425	0.033	-0.29	56
LUAD	hsa-miR-139-5p	MIMAT0000250	0.021	-0.3	60
LUAD	hsa-miR-27b-3p	MIMAT0000419	0.0042	-0.37	60

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TissGeneMut for ARX

TissGeneSNV for ARX

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.E241Q	CESC	1
p.E560D	UCEC	1
p.V561L	LIHC	1
p.G286A	GBM	1
p.E320K	SKCM	1
p.A302D	UCS	1
p.S317R	LUAD	1
p.E342K	SKCM	1
p.Q48L	LIHC	1
p.E360K	ESCA	1
p.S26F	STAD	1
p.G34R	COAD	1
p.H298N	THCA	1
p.R42W	STAD	1
p.R35Q	SKCM	1
p.E61K	SKCM	1
p.R364W	BLCA	1
p.P299S	TGCT	1
p.L23F	LUAD	1
p.C10S	LIHC	1
p.R371P	HNSC	1
p.L365M	READ	1
p.L24R	COAD	1
p.A534V	UCEC	1

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TissGeneCNV for ARX

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 ARX

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

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TissGeneNet for ARX

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)

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TissGeneProg for ARX

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 ARX

TissGeneDrug for ARX

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 ARX

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

Disease ID	Disease name	# pubmeds	Source
umls:C0025362	Mental Retardation	24	BeFree
umls:C0037769	West Syndrome	21	BeFree,LHGDN,ORPHANET
umls:C1136249	Mental Retardation, X-Linked	21	BeFree,LHGDN
umls:C0014544	Epilepsy	17	BeFree
umls:C3714756	Intellectual Disability	15	BeFree,LHGDN
umls:C1848199	X-Linked Lissencephaly	14	BeFree
umls:C2931919	X-linked infantile spasm syndrome	9	BeFree
umls:C0266463	Lissencephaly	8	BeFree,LHGDN
umls:C0027765	nervous system disorder	7	BeFree
umls:C0393706	Early infantile epileptic encephalopathy with suppression bursts	7	BeFree,ORPHANET
umls:C0013421	Dystonia	6	BeFree,LHGDN
umls:C0014550	Epilepsies, Myoclonic	5	BeFree,LHGDN
umls:C0175754	Agenesis of corpus callosum	5	BeFree
umls:C0266362	Ambiguous Genitalia	4	BeFree
umls:C0393593	Dystonia Disorders	4	BeFree
umls:C0424605	Developmental delay (disorder)	4	BeFree
umls:C0000768	Congenital Abnormality	3	BeFree
umls:C0036572	Seizures	3	BeFree,LHGDN
umls:C0220775	RUSSELL-SILVER SYNDROME, X-LINKED	3	BeFree
umls:C0543888	Epileptic encephalopathy	3	BeFree
umls:C0796250	PARTINGTON X-LINKED MENTAL RETARDATION SYNDROME	3	BeFree,CLINVAR,CTD_human,ORPHANET
umls:C0026650	Movement Disorders	2	BeFree,LHGDN
umls:C0036857	Severe mental retardation (I.Q. 20-34)	2	BeFree
umls:C0266449	Congenital anomaly of brain	2	BeFree
umls:C1096063	Drug Resistant Epilepsy	2	BeFree
umls:C1846171	Lissencephaly, X-Linked, 2	2	CLINVAR,CTD_human,MGD,ORPHANET,UNIPROT
umls:C1848954	Generalized dystonia	2	BeFree
umls:C2931498	Mental Retardation, X-Linked 1	2	BeFree
umls:C0004352	Autistic Disorder	1	BeFree,GAD,LHGDN
umls:C0011860	Diabetes Mellitus, Non-Insulin-Dependent	1	RGD
umls:C0011991	Diarrhea	1	BeFree
umls:C0020225	Hydranencephaly	1	BeFree
umls:C0020255	Hydrocephalus	1	LHGDN
umls:C0026106	Mild Mental Retardation	1	BeFree
umls:C0158687	Congenital malformation of genital organs	1	BeFree
umls:C0221760	brain cyst	1	BeFree
umls:C0234523	Apraxia, Ideomotor	1	BeFree
umls:C0235946	Cerebral atrophy	1	BeFree
umls:C0242350	Erectile dysfunction	1	GAD
umls:C0265219	Miller Dieker syndrome	1	BeFree
umls:C0270742	Athetoid cerebral palsy	1	BeFree
umls:C0393698	Cryptogenic Infantile Spasms	1	BeFree
umls:C0796124	Proud Syndrome	1	CLINVAR,CTD_human,ORPHANET,UNIPROT
umls:C0796244	MENTAL RETARDATION, X-LINKED, WITH OR WITHOUT SEIZURES, ARX-RELATED (disorder)	1	CLINVAR,CTD_human,UNIPROT
umls:C1510586	Autism Spectrum Disorders	1	BeFree
umls:C1837249	Malformations of Cortical Development, Group II	1	BeFree
umls:C3463992	EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 1	1	CLINVAR,CTD_human,MGD,ORPHANET,UNIPROT