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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 HELLS
check button Gene summary
Basic gene informationGene symbolHELLS
Gene namehelicase, lymphoid-specific
SynonymsLSH|PASG|SMARCA6
CytomapUCSC genome browser: 10q24.2
Type of geneprotein-coding
RefGenesNM_001289067.1,
NM_001289068.1,NM_001289069.1,NM_001289070.1,NM_001289071.1,
NM_001289072.1,NM_001289073.1,NM_001289074.1,NM_001289075.1,
NM_018063.4,
DescriptionSWI/SNF2-related matrix-associated actin-dependent regulator of chromatin subfamily A member 6SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6lymphoid-specific helicaseproliferation-associated SNF2-like
Modification date20141207
dbXrefs MIM : 603946
HGNC : HGNC
Ensembl : ENSG00000119969
HPRD : 07232
Vega : OTTHUMG00000018793
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HELLS
BioGPS: 3070
PathwayNCI Pathway Interaction Database: HELLS
KEGG: HELLS
REACTOME: HELLS
Pathway Commons: HELLS
ContextiHOP: HELLS
ligand binding site mutation search in PubMed: HELLS
UCL Cancer Institute: HELLS
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)Bone marrowTestis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LAMLTGCT
Reference showing the relevant tissue of HELLS
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.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID


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TissGeneExp for HELLS

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
COAD0.428977643-1.2969262031.7259038466.75E-119.93E-10
BRCA-0.27763592-2.2938210072.0161850887.05E-309.32E-29
LUAD-0.697956972-3.4598500762.7618931031.00E-265.61E-25
LUSC0.570507734-3.1450706983.7155784311.33E-374.28E-35
HNSC0.219433725-0.8680430191.0874767444.56E-073.81E-06
STAD0.478999278-1.8556507222.334655.26E-092.96E-07
LIHC-2.131304972-4.2679989722.1366948.73E-121.42E-10
ESCA0.950088482-1.1645478812.1146363640.0003910.008168145
BLCA0.294906186-1.9438885512.2387947370.0001720.001685145
KICH-2.635332972-1.379064972-1.2562687.96E-050.000212653


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TissGene-miRNA for HELLS

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


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TissGeneMut for HELLS
TissGeneSNV for HELLS

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.W225CTHYM1
p.R568CSKCM1
p.R675*BLCA1
p.R735KLIHC1
p.A482TSKCM1
p.L275PLGG1
p.K254NTHYM1
p.E527AKIRC1
p.R511QREAD1
p.T505ALUAD1
p.N398KUCEC1
p.E229KCOAD1
p.P201SSKCM1
p.S179LUCEC1
p.R365CBLCA1
p.K763NUCEC1
p.A342VCOAD1
p.G11DSTAD1
p.G253DMESO1
p.N764TUCEC1
p.L168FSKCM1
p.I822MTHCA1
p.F198SSKCM1
p.D729NUCEC1
p.R510LHNSC1
p.R340QREAD1
p.M86ISKCM1
p.S643NUCEC1
p.E593*PAAD1
p.E87KSKCM1
p.E593XPAAD1
p.E798DKIRP1
p.Q442*HNSC1
p.N114HUCEC1
p.T27SLUAD1
p.R309HHNSC1
p.K103NBLCA1
p.S179LSKCM1
p.R53HCOAD1
p.F198VSKCM1
p.T84MSARC1
p.Y651CSTAD1
p.K204RLUAD1
p.R224QHNSC1
p.R707KSTAD1
p.P716SUCEC1
p.R510XLIHC1
p.R675*ACC1
p.D426YUCEC1
p.N517HCOAD1
p.L42VBLCA1
p.E98*UCEC1
p.H303YBLCA1
p.R319WSTAD1
p.R803QUCEC1
p.D629NESCA1
p.Y65HSTAD1
p.I732SUCS1
p.R849QCESC1
p.I147MPRAD1
p.V210ICOAD1
p.P385HESCA1
p.R803QLGG1
p.V228ISTAD1
p.E818DUCEC1


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TissGeneCNV for HELLS

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 HELLS

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
Chimerdb3.0ChiTaRsNAAU136737AIM1-HELLSchr6:106978190chr10:96347986
Chimerdb3.0ChiTaRsNABE077006EIF4G1-HELLSchr3:184052470chr10:96326010
Chimerdb3.0ChiTaRsNACN480729RTN3-HELLSchr11:63526522chr10:96313882
TCGAfusionPortalPRADABRCATCGA-A8-A09Q-01AHELLS-TBC1D12In-frameChr10:96348147Chr10:96281712


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TissGeneNet for HELLS

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)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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COAD (tumor)COAD (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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HNSC (tumor)HNSC (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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KICH (tumor)KICH (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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KIRC (tumor)KIRC (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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KIRP (tumor)KIRP (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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LIHC (tumor)LIHC (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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LUAD (tumor)LUAD (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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LUSC (tumor)LUSC (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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PRAD (tumor)PRAD (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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STAD (tumor)STAD (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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THCA (tumor)THCA (normal)
HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (tumor)HELLS, MAGEA6, SUMO2, HDAC2, HDAC1, MYC, CIAO1, DNMT3B, RPAP3, DNMT1, RPAP2 (normal)
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TissGeneProg for HELLS

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 HELLS
TissGeneDrug for HELLS

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


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TissGeneDisease for HELLS

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C1168401Squamous cell carcinoma of the head and neck4BeFree
umls:C0006142Malignant neoplasm of breast1BeFree
umls:C0007131Non-Small Cell Lung Carcinoma1BeFree
umls:C0009402Colorectal Carcinoma1BeFree
umls:C0024623Malignant neoplasm of stomach1BeFree
umls:C0026948Mycosis Fungoides1BeFree
umls:C0032460Polycystic Ovary Syndrome1CTD_human
umls:C0035335Retinoblastoma1BeFree
umls:C0036920Sezary Syndrome1BeFree
umls:C0178874Tumor Progression1BeFree
umls:C0677886Epithelial ovarian cancer1GAD
umls:C0678222Breast Carcinoma1BeFree
umls:C0686619Secondary malignant neoplasm of lymph node1BeFree
umls:C0699791Stomach Carcinoma1BeFree
umls:C1134719Invasive Ductal Breast Carcinoma1BeFree
umls:C1518171Malignant Conversion1BeFree
umls:C1527249Colorectal Cancer1BeFree