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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 SIM1
check button Gene summary
Basic gene informationGene symbolSIM1
Gene namesingle-minded family bHLH transcription factor 1
SynonymsbHLHe14
CytomapUCSC genome browser: 6q16.3
Type of geneprotein-coding
RefGenesNM_005068.2,
Descriptionclass E basic helix-loop-helix protein 14single-minded homolog 1
Modification date20141207
dbXrefs MIM : 603128
HGNC : HGNC
Ensembl : ENSG00000112246
HPRD : 07049
Vega : OTTHUMG00000015275
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SIM1
BioGPS: 6492
PathwayNCI Pathway Interaction Database: SIM1
KEGG: SIM1
REACTOME: SIM1
Pathway Commons: SIM1
ContextiHOP: SIM1
ligand binding site mutation search in PubMed: SIM1
UCL Cancer Institute: SIM1
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)KidneyPancreas
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)KIRC,KIRP,KICHPAAD
Reference showing the relevant tissue of SIM1
Description by TissGene annotationsRisk TissGene in RFS
TissgsKTS
CNV lost TissGeneKTS
* 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 SIM1

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
KIRP4.0108626346.407075134-2.39621251.04E-054.33E-05
KIRC2.3085227036.96300187-4.6544791674.43E-224.04E-21
BRCA0.5125254082.097379794-1.5848543864.94E-081.52E-07
PRAD-2.461974626-1.233022703-1.2289519230.001460.004475869


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TissGene-miRNA for SIM1

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 SIM1
TissGeneSNV for SIM1

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.R425KSKCM2
p.G638ESKCM2
p.G303SSTAD2
p.R665CSKCM2
p.E544KSKCM2
p.V213MCESC2
p.V222ISTAD2
p.S428FSKCM2
p.H394YSKCM2
p.S382*BLCA1
p.D202NSKCM1
p.H523NLGG1
p.W490LKIRC1
p.R397KSKCM1
p.H315YPRAD1
p.S409RESCA1
p.Q704RHNSC1
p.S343FLUSC1
p.Q748HESCA1
p.N626IHNSC1
p.E224KLUSC1
p.G113DUCEC1
p.T481MCOAD1
p.R636TLUSC1
p.K600ISKCM1
p.W490*SKCM1
p.D413NBLCA1
p.S443RSARC1
p.I682MSTAD1
p.E126DCOAD1
p.E399KSKCM1
p.G179SSTAD1
p.P539RGBM1
p.V94MLGG1
p.E645KSKCM1
p.A280TGBM1
p.P257TSTAD1
p.H632RHNSC1
p.G113SHNSC1
p.Q152KBRCA1
p.N697SUCEC1
p.L592QBLCA1
p.S433LHNSC1
p.S391LPRAD1
p.S536YUCEC1
p.S663LREAD1
p.A236SLUAD1
p.R296MUCEC1
p.K190NLIHC1
p.E560KSKCM1
p.I156VLUAD1
p.S391LSKCM1
p.A517TLGG1
p.K287NLUSC1
p.D424NPRAD1
p.A450VSKCM1
p.S541LSTAD1
p.R548QREAD1
p.N697HSARC1
p.W490XSKCM1
p.P352TCOAD1
p.V328IHNSC1
p.T264NOV1
p.E155KSKCM1
p.E579DOV1
p.S680LUCEC1
p.H685YSKCM1
p.A494TBRCA1
p.S31LBLCA1
p.G475SSKCM1
p.N580KLUSC1
p.A587TSTAD1
p.S35LSKCM1
p.R548QSKCM1
p.G370RSKCM1
p.L745MESCA1
p.L175FLUAD1
p.T412PLUAD1
p.H738QLUAD1
p.E336KREAD1
p.P426RLUAD1
p.G121RSTAD1
p.H685RSTAD1
p.W528LBLCA1
p.V326ISTAD1
p.V76ISTAD1
p.R10QUCEC1
p.H527NLUAD1
p.R521SBLCA1
p.G187STHYM1
p.P72LSKCM1
p.Q748HLUAD1
p.L285MPRAD1
p.A169TPAAD1
p.S319TKIRP1
p.E62KSKCM1
p.G59_spliceGBM1
p.G203SUCEC1
p.S382FSKCM1
p.V151MUCEC1
p.P417QLUAD1
p.S724RHNSC1
p.V326ISKCM1
p.S440LSKCM1
p.N596ITHCA1
p.S380LHNSC1
p.M164TCOAD1
p.D431NSKCM1
p.D590HBLCA1
p.D424NSKCM1
p.I104TLIHC1
p.K576XTHYM1
p.S35LHNSC1
p.Y103CUCEC1
p.D590ELUAD1
p.L298VLUSC1
p.F739ISTAD1
p.A607VHNSC1
p.L168FLUAD1
p.A450VSTAD1
p.S31LUCEC1
p.P588LLUSC1
p.D134GSTAD1
p.S18NUCEC1
p.W528CLUAD1
p.A435TGBM1
p.S31LCESC1
p.E510KSKCM1
p.R548XCOAD1
p.D431EBLCA1
p.T726ISKCM1
p.T107AHNSC1
p.Q341HLUSC1
p.S31LHNSC1
p.G271CUCEC1
p.P417SSKCM1
p.P561HLUAD1
p.E224KSKCM1
p.D246GREAD1
p.I762MSKCM1
p.R550CSKCM1
p.P30ASTAD1
p.E118XACC1
p.S454LSKCM1
p.P661LSKCM1
p.G597ESKCM1
p.R728SLUAD1
p.Y295*LUSC1
p.E224DCOAD1
p.A371VCOAD1
p.N596DSKCM1
p.I564SLUAD1
p.G638RSKCM1
p.E135VSTAD1
p.C619FUCEC1
p.P539LSKCM1
p.A542THNSC1
p.S382CBLCA1
p.V519IREAD1
p.H463YSKCM1
p.D431NHNSC1
p.K379RLGG1
p.D366NBLCA1
p.T758PHNSC1
p.S105LLUAD1
p.E579*LUSC1
p.V222IHNSC1
p.S320FBRCA1
p.R548*GBM1
p.Q635HESCA1
p.Q611HLUAD1
p.L60ISARC1
p.R158HUCEC1
p.L277RLIHC1
p.T763AHNSC1
p.S71NGBM1
p.S67*HNSC1
p.D239HBRCA1


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TissGeneCNV for SIM1

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 SIM1

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
Chimerdb3.0ChiTaRsNADB024801BRK1-SIM1chr3:10168138chr6:100841581
Chimerdb3.0FusionScanLUSCTCGA-46-6026-01APREP-SIM1In-Framechr6:105736632chr6:100868834
TCGAfusionPortalPRADALUADTCGA-69-7760-01ASIM1-ASCC3In-frameChr6:100868666Chr6:100988263


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TissGeneNet for SIM1

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)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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COAD (tumor)COAD (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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HNSC (tumor)HNSC (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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KICH (tumor)KICH (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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KIRC (tumor)KIRC (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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KIRP (tumor)KIRP (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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LIHC (tumor)LIHC (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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LUAD (tumor)LUAD (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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LUSC (tumor)LUSC (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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PRAD (tumor)PRAD (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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STAD (tumor)STAD (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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THCA (tumor)THCA (normal)
SIM1, HSP90AA1, ARNT (tumor)SIM1, HSP90AA1, ARNT (normal)
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TissGeneProg for SIM1

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 SIM1
TissGeneDrug for SIM1

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 SIM1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0028754Obesity15BeFree,CTD_human,GAD,MGD
umls:C0028756Obesity, Morbid7BeFree
umls:C0032897Prader-Willi Syndrome3BeFree
umls:C0020505Hyperphagia2BeFree
umls:C0424605Developmental delay (disorder)2BeFree
umls:C3809877PRADER-WILLI-LIKE SYNDROME2BeFree
umls:C0020456Hyperglycemia1CTD_human
umls:C0023015Language Disorders1BeFree
umls:C0027627Neoplasm Metastasis1BeFree
umls:C0031117Peripheral Neuropathy1CTD_human
umls:C0036341Schizophrenia1GAD
umls:C0333875High-Grade Squamous Intraepithelial Lesions1BeFree
umls:C0497406Overweight1BeFree
umls:C1302773Low Grade Squamous Intraepithelial Neoplasia1BeFree
umls:C1458155Mammary Neoplasms1CTD_human