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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 SIM2
check button Gene summary
Basic gene informationGene symbolSIM2
Gene namesingle-minded family bHLH transcription factor 2
SynonymsHMC13F06|HMC29C01|SIM|bHLHe15
CytomapUCSC genome browser: 21q22.13
Type of geneprotein-coding
RefGenesNM_005069.4,
NM_009586.3,
Descriptionclass E basic helix-loop-helix protein 15single-minded homolog 2transcription factor SIM2
Modification date20141207
dbXrefs MIM : 600892
HGNC : HGNC
Ensembl : ENSG00000159263
HPRD : 02935
Vega : OTTHUMG00000086637
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SIM2
BioGPS: 6493
PathwayNCI Pathway Interaction Database: SIM2
KEGG: SIM2
REACTOME: SIM2
Pathway Commons: SIM2
ContextiHOP: SIM2
ligand binding site mutation search in PubMed: SIM2
UCL Cancer Institute: SIM2
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)ColonKidneyOvary
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)COADKIRC,KIRP,KICHOV
Reference showing the relevant tissue of SIM2
Description by TissGene annotationsRisk TissGene in OS
* 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 SIM2

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
BRCA-0.556166834-1.5892185891.0330517542.74E-088.67E-08
KIRP-1.6055126682.261959207-3.8674718752.20E-145.36E-13
HNSC-1.0880757490.841221925-1.9292976745.37E-063.29E-05
KIRC-2.2297793342.204623443-4.4344027786.44E-433.28E-41
KICH-3.3664581682.874969832-6.2414281.09E-152.58E-14
LUSC-0.329728599-2.4028403642.0731117655.96E-122.55E-11
PRAD3.8474709860.6145652173.2329057697.55E-182.11E-15
COAD0.874819063-2.9014117063.7762307691.31E-161.30E-14
BLCA1.098791937-1.1406238522.2394157892.31E-071.07E-05


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TissGene-miRNA for SIM2

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 SIM2
TissGeneSNV for SIM2

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.H276YSKCM2
p.A63VCOAD2
p.G113CKIRP1
p.S503YCESC1
p.D273NSKCM1
p.F234LBLCA1
p.F232LBLCA1
p.K368NCESC1
p.R318HCHOL1
p.V313ALUAD1
p.F160LLUAD1
p.G487RSKCM1
p.F91IKIRC1
p.D134NLUAD1
p.R544QCOAD1
p.R163*BRCA1
p.F394SLIHC1
p.A485VLUAD1
p.Y194HSKCM1
p.S237GPRAD1
p.S109FBLCA1
p.L240PLIHC1
p.A40VLUSC1
p.Q308HHNSC1
p.T223ISKCM1
p.N384SSKCM1
p.A8VDLBC1
p.R163*UCEC1
p.Q215RLIHC1
p.A212VCOAD1
p.R171GLUAD1
p.L369SKIRP1
p.S159*LUAD1
p.A221TSTAD1
p.H267YSKCM1
p.D202NACC1
p.L340FUVM1
p.P512QESCA1
p.R158MLGG1
p.S343YLUAD1
p.A9TBLCA1
p.R318HSTAD1
p.E262KSKCM1
p.T120MGBM1
p.S355FLUSC1
p.W304CSKCM1
p.M198LOV1
p.V76IHNSC1
p.K190NUCEC1
p.S5CHNSC1
p.M164ISKCM1
p.D246NSKCM1


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TissGeneCNV for SIM2

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 SIM2

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
Chimerdb3.0FusionScanBRCATCGA-BH-A1EY-01APTTG1IP-SIM2In-Framechr21:46293416chr21:38081467
Chimerdb3.0FusionScanESCATCGA-L5-A891-01ASIM2-MORC3Out-of-Framechr21:38103452chr21:37721608
Chimerdb3.0FusionScanCOADTCGA-A6-5656-01ACD9-SIM2Out-of-Framechr12:6334700chr21:38084832
TCGAfusionPortalPRADABRCATCGA-BH-A1EY-01APTTG1IP-SIM2In-frameChr21:46293417Chr21:38081468
TCGAfusionPortalPRADALGGTCGA-DU-6406-01ASIM2-KCNJ6CDS-5UTRChr21:38072221Chr21:39213011


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TissGeneNet for SIM2

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)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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COAD (tumor)COAD (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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HNSC (tumor)HNSC (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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KICH (tumor)KICH (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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KIRC (tumor)KIRC (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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KIRP (tumor)KIRP (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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LIHC (tumor)LIHC (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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LUAD (tumor)LUAD (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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LUSC (tumor)LUSC (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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PRAD (tumor)PRAD (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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STAD (tumor)STAD (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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THCA (tumor)THCA (normal)
SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (tumor)SIM2, UBC, PARK2, ARNT, ARIH1, ARNT2 (normal)
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TissGeneProg for SIM2

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 SIM2
TissGeneDrug for SIM2

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 SIM2

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0013080Down Syndrome14BeFree,CTD_human,LHGDN
umls:C1860787DOWN SYNDROME CRITICAL REGION5BeFree
umls:C1956346Coronary Artery Disease4BeFree
umls:C0017638Glioma3BeFree
umls:C0007095Carcinoid Tumor2BeFree
umls:C0009375Colonic Neoplasms2BeFree
umls:C0025362Mental Retardation2BeFree
umls:C0033578Prostatic Neoplasms2BeFree
umls:C0272138Erythroblastosis2BeFree
umls:C0280100Solid tumour2BeFree
umls:C0699790Colon Carcinoma2BeFree
umls:C1458155Mammary Neoplasms2LHGDN
umls:C0006118Brain Neoplasms1BeFree
umls:C0006142Malignant neoplasm of breast1BeFree
umls:C0007102Malignant tumor of colon1BeFree
umls:C0008925Cleft Palate1CTD_human
umls:C0017636Glioblastoma1BeFree
umls:C0020443Hypercholesterolemia1BeFree
umls:C0024291Lymphohistiocytosis, Hemophagocytic1BeFree
umls:C0026470Monoclonal Gammopathy of Undetermined Significance1BeFree
umls:C0026764Multiple Myeloma1BeFree
umls:C0036439Scoliosis, unspecified1GAD
umls:C0079541Holoprosencephaly1BeFree
umls:C0151786Muscle Weakness1CTD_human
umls:C0235974Pancreatic carcinoma1BeFree
umls:C0346647Malignant neoplasm of pancreas1BeFree
umls:C0376358Malignant neoplasm of prostate1BeFree
umls:C0376634Craniofacial Abnormalities1CTD_human
umls:C0600139Prostate carcinoma1BeFree
umls:C0678222Breast Carcinoma1BeFree
umls:C1297882Partial Trisomy1BeFree
umls:C2745900Promyelocytic leukemia1BeFree
umls:C2937421Prostatic Hyperplasia1LHGDN
umls:C3714756Intellectual Disability1LHGDN