TissGDB

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

TissGeneSummary for GTF2A1L

Gene summary

Basic gene information	Gene symbol	GTF2A1L
	Gene name	general transcription factor IIA, 1-like
	Synonyms	ALF
	Cytomap	UCSC genome browser: 2p16.3
	Type of gene	protein-coding
	RefGenes	NM_001193487.2, NM_006872.4,NM_172196.1,
	Description	GTF2A1-like factorTFIIA large subunit isoform ALFTFIIA-alpha and beta-like factorTFIIA-alpha/beta-like factorgeneral transcription factor II A, 1-like factor
	Modification date	20141207
dbXrefs	MIM : 605358
	HGNC : HGNC
	Ensembl : ENSG00000242441
	HPRD : 05640
	Vega : OTTHUMG00000152038
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GTF2A1L
	BioGPS: 11036
Pathway	NCI Pathway Interaction Database: GTF2A1L
	KEGG: GTF2A1L
	REACTOME: GTF2A1L
	Pathway Commons: GTF2A1L
Context	iHOP: GTF2A1L
	ligand binding site mutation search in PubMed: GTF2A1L
	UCL Cancer Institute: GTF2A1L
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 GTF2A1L
Description by TissGene annotations	Cancer gene

* 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 GTF2A1L

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	-2.296550925	-0.487214925	-1.809336	2.12E-06	7.54E-06
HNSC	-1.016056971	-2.376296506	1.360239535	6.86E-06	4.09E-05
STAD	-2.302414675	-0.984152175	-1.3182625	0.00686	0.025250638
BLCA	-0.908791977	1.38118697	-2.289978947	8.40E-05	0.000948305
LUSC	-0.307061121	-1.433563082	1.126501961	0.000321	0.000634116
KIRP	-2.271820925	-0.854020925	-1.4178	3.01E-05	0.000115358

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TissGene-miRNA for GTF2A1L

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 GTF2A1L

TissGeneSNV for GTF2A1L

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.E371K	SKCM	2
p.D38Y	READ	1
p.A271T	READ	1
p.D434N	SKCM	1
p.V468A	READ	1
p.G305E	SKCM	1
p.D457N	SKCM	1
p.R302K	SKCM	1
p.L180V	READ	1
p.G378E	SKCM	1
p.E185G	READ	1
p.E237K	SKCM	1
p.R447I	UCEC	1
p.P229A	COAD	1
p.D380G	SKCM	1
p.P154L	SKCM	1
p.C234R	READ	1
p.Y441X	COAD	1
p.Y91*	UCEC	1
p.D405Y	READ	1
p.E345K	SKCM	1
p.L299P	SKCM	1
p.G362E	SKCM	1
p.R337Q	COAD	1
p.Q252H	COAD	1
p.T45I	SKCM	1
p.V141M	SKCM	1
p.V383I	SKCM	1
p.N259D	COAD	1

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TissGeneCNV for GTF2A1L

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 GTF2A1L

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	BC101772	STON1-GTF2A1L		chr2:48598515	chr2:48617798
Chimerdb3.0	FusionScan	HNSC	TCGA-CN-6019-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	PRAD	TCGA-G9-6362-11A	STON1-GTF2A1L	In-Frame	chr2:48818994	chr2:48872171
Chimerdb3.0	FusionScan	LGG	TCGA-QH-A870-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	KIRC	TCGA-BP-4173-01A	STON1-GTF2A1L	In-Frame	chr2:48809702	chr2:48869540
Chimerdb3.0	FusionScan	KIRC	TCGA-B0-5693-01A	STON1-GTF2A1L	In-Frame	chr2:48818994	chr2:48872171
Chimerdb3.0	FusionScan	KIRC	TCGA-DV-5576-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	BRCA	TCGA-A2-A0SX-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	BRCA	TCGA-AC-A8OS-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	BRCA	TCGA-AR-A2LR-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	BRCA	TCGA-D8-A1J8-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	BRCA	TCGA-BH-A203-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48896860
Chimerdb3.0	FusionScan	BRCA	TCGA-D8-A1XO-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	BRCA	TCGA-E2-A10E-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757968	chr2:48873591
Chimerdb3.0	FusionScan	BRCA	TCGA-E2-A153-11A	STON1-GTF2A1L	In-Frame	chr2:48818994	chr2:48872171
Chimerdb3.0	FusionScan	BRCA	TCGA-A8-A0AB-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	BRCA	TCGA-BH-A1FN-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	ESCA	TCGA-LN-A9FP-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757968	chr2:48848305
Chimerdb3.0	FusionScan	ESCA	TCGA-IG-A3I8-11A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48847989
Chimerdb3.0	FusionScan	ESCA	TCGA-LN-A4A8-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757968	chr2:48848305
Chimerdb3.0	FusionScan	ESCA	TCGA-V5-A7RC-06A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48847989
Chimerdb3.0	FusionScan	LUAD	TCGA-05-4398-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	LUAD	TCGA-38-4630-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	LUAD	TCGA-50-5946-02A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305
Chimerdb3.0	FusionScan	LUSC	TCGA-98-A53D-01A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757968	chr2:48848305
Chimerdb3.0	FusionScan	LUSC	TCGA-34-8454-11A	STON1-GTF2A1L	5'UTR-CDS	chr2:48757355	chr2:48848305

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TissGeneNet for GTF2A1L

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)
GTF2A1L, CSNK2A1, TBP, CSNK2A2, SUB1, CEBPE, MAFF, EMX2, HOXA5, MAFG, HOXC11, TLX3, ATF4, ID3, GTF2A2, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, SIX6 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, SUB1, CEBPE, MAFF, EMX2, HOXA5, MAFG, HOXC11, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, NKX2-3, EMX1, HOXC9, SIX6 (normal)

COAD (tumor)	COAD (normal)
GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, MAFF, EMX2, HOXA5, MAFG, HOXC11, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, TLX2 (tumor)	GTF2A1L, CSNK2A1, PAX9, SUB1, CEBPE, MAFF, EMX2, HOXA5, HOXC11, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, SIX6, TLX2 (normal)

HNSC (tumor)	HNSC (normal)
GTF2A1L, CSNK2A1, TBP, PAX9, SUB1, CEBPE, MAFF, EMX2, HOXA5, MAFG, HOXC11, TLX3, ATF4, ID3, GTF2A2, ASCL3, HMG20A, NKX2-3, HOXC9, SIX6, TLX2 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, MAFF, EMX2, HOXA5, MAFG, HOXC11, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, NKX2-3, EMX1, HOXC9, SIX6, TLX2 (normal)

KICH (tumor)	KICH (normal)
GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, MAFF, EMX2, HOXA5, MAFG, HOXC11, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, EMX1, HOXC9, SIX6, TLX2 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, MAFF, EMX2, MAFG, HOXC11, TLX3, ATF4, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, TLX2 (normal)

KIRC (tumor)	KIRC (normal)
GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, MAFF, EMX2, HOXA5, MAFG, HOXC11, TLX3, ATF4, ID3, GTF2A2, ASCL3, HMG20A, HOXC9, SIX6, TLX2 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, EMX2, HOXA5, MAFG, HOXC11, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, NKX2-3, EMX1, HOXC9, TLX2 (normal)

KIRP (tumor)	KIRP (normal)
GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, MAFF, EMX2, HOXA5, MAFG, HOXC11, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, SIX6, TLX2 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, MAFF, EMX2, HOXA5, MAFG, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, HOXC9, SIX6, TLX2 (normal)

LIHC (tumor)	LIHC (normal)
GTF2A1L, CSNK2A1, CSNK2A2, PAX9, SUB1, CEBPE, MAFF, EMX2, HOXA5, MAFG, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, TLX2 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, MAFF, EMX2, HOXA5, HOXC11, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, HOXC9, SIX6, TLX2 (normal)

LUAD (tumor)	LUAD (normal)
GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, MAFF, EMX2, HOXA5, HOXC11, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, NKX2-3, EMX1, HOXC9, SIX6 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, MAFF, EMX2, HOXA5, MAFG, TLX3, ATF4, ID3, GTF2A2, ZBTB3, HMG20A, NKX2-3, EMX1, HOXC9, SIX6 (normal)

LUSC (tumor)	LUSC (normal)
GTF2A1L, CSNK2A1, CSNK2A2, PAX9, SUB1, CEBPE, MAFF, EMX2, HOXA5, HOXC11, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, SIX6, TLX2 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, MAFF, HOXA5, MAFG, HOXC11, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, TLX2 (normal)

PRAD (tumor)	PRAD (normal)
GTF2A1L, CSNK2A1, TBP, PAX9, SUB1, MAFF, EMX2, HOXA5, MAFG, HOXC11, TLX3, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, SIX6, TLX2 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, MAFF, EMX2, MAFG, HOXC11, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, SIX6 (normal)

STAD (tumor)	STAD (normal)
GTF2A1L, CSNK2A1, CSNK2A2, PAX9, CEBPE, MAFF, EMX2, HOXA5, MAFG, HOXC11, TLX3, ATF4, ID3, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, SIX6, TLX2 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, EMX2, HOXA5, MAFG, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, SIX6 (normal)

THCA (tumor)	THCA (normal)
GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, SUB1, CEBPE, EMX2, HOXA5, MAFG, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, SIX6, TLX2 (tumor)	GTF2A1L, CSNK2A1, TBP, CSNK2A2, PAX9, CEBPE, MAFF, EMX2, HOXA5, TLX3, ATF4, ID3, GTF2A2, ZBTB3, ASCL3, HMG20A, NKX2-3, EMX1, HOXC9, SIX6, TLX2 (normal)

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TissGeneProg for GTF2A1L

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 GTF2A1L

TissGeneDrug for GTF2A1L

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 GTF2A1L

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

Disease ID	Disease name	# pubmeds	Source
umls:C0004134	Ataxia	1	BeFree
umls:C0004509	Azoospermia	1	BeFree
umls:C0019163	Hepatitis B	1	BeFree
umls:C0019196	Hepatitis C	1	BeFree
umls:C0021364	Male infertility	1	BeFree
umls:C0023895	Liver diseases	1	BeFree
umls:C0025362	Mental Retardation	1	BeFree
umls:C0028960	Oligospermia	1	BeFree
umls:C0040336	Tobacco Use Disorder	1	GAD
umls:C0162557	Liver Failure, Acute	1	BeFree
umls:C0751157	FRAXE Syndrome	1	BeFree
umls:C2239176	Liver carcinoma	1	BeFree