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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 MSI1
check button Gene summary
Basic gene informationGene symbolMSI1
Gene namemusashi RNA-binding protein 1
Synonyms-
CytomapUCSC genome browser: 12q24
Type of geneprotein-coding
RefGenesNM_002442.3,
DescriptionRNA-binding protein Musashi homolog 1musashi-1musashi1
Modification date20141207
dbXrefs MIM : 603328
HGNC : HGNC
Ensembl : ENSG00000135097
HPRD : 04509
Vega : OTTHUMG00000169344
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MSI1
BioGPS: 4440
PathwayNCI Pathway Interaction Database: MSI1
KEGG: MSI1
REACTOME: MSI1
Pathway Commons: MSI1
ContextiHOP: MSI1
ligand binding site mutation search in PubMed: MSI1
UCL Cancer Institute: MSI1
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)TestisEye
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)TGCTUVM
Reference showing the relevant tissue of MSI1
Description by TissGene annotationsHave 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.

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


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TissGeneExp for MSI1

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
PRAD3.6551507832.6345353981.0206153853.79E-095.18E-08
LUSC1.626793731-1.2187023472.8454960781.10E-104.14E-10
BLCA0.667534082-1.5885080232.2560421050.005080.026709031
HNSC0.144246444-1.0617163461.2059627910.006020.015860656
LIHC0.069858398-1.2797736021.3496320.003420.008193981
LUAD0.032863846-0.9997413261.0326051720.00140.002993518
KIRP-1.6100896020.079204148-1.689293750.0001060.000358991


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TissGene-miRNA for MSI1

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
UCShsa-miR-138-5pMIMAT00004300.038-0.2856
ACChsa-miR-490-3pMIMAT00028060.01-0.2978
ACChsa-miR-490-3pMIMAT00028060.01-0.2978
LUADhsa-miR-125a-5pMIMAT00004430.0066-0.3560
UCShsa-miR-137MIMAT00004290.021-0.3656
UCShsa-miR-181d-5pMIMAT00028210.0057-0.3756


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TissGeneMut for MSI1
TissGeneSNV for MSI1

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.G234VLGG2
p.G153WLIHC1
p.Y361SPAAD1
p.T292MHNSC1
p.M207ISKCM1
p.G73RKIRC1
p.P254QSKCM1
p.Y361HSTAD1
p.K187NCOAD1
p.V163MESCA1
p.P244HTHYM1
p.F68VESCA1
p.I169NKIRP1
p.P254QHNSC1
p.D91NLUSC1
p.K183NTHCA1
p.V66FTHCA1
p.R98QTHCA1
p.R107*UCEC1
p.P313LSKCM1
p.P254SSKCM1
p.K110MSKCM1
p.P192SBRCA1
p.V66AUCEC1
p.N175SSTAD1
p.S229RBRCA1


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TissGeneCNV for MSI1

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 MSI1

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
TCGAfusionPortalPRADAHNSCTCGA-CV-7253-01APXN-MSI1CDS-3UTRChr12:120659426Chr12:120780908
TCGAfusionPortalPRADALUADTCGA-55-7570-01APXN-MSI1Out-of-frameChr12:120703420Chr12:120802558
TCGAfusionPortalPRADALUSCTCGA-34-5232-01AC12orf34-MSI15UTR-CDSChr12:110152702Chr12:120802558


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TissGeneNet for MSI1

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)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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COAD (tumor)COAD (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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HNSC (tumor)HNSC (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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KICH (tumor)KICH (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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KIRC (tumor)KIRC (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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KIRP (tumor)KIRP (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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LIHC (tumor)LIHC (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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LUAD (tumor)LUAD (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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LUSC (tumor)LUSC (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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PRAD (tumor)PRAD (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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STAD (tumor)STAD (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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THCA (tumor)THCA (normal)
MSI1, PNMA1 (tumor)MSI1, PNMA1 (normal)
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TissGeneProg for MSI1

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 MSI1
TissGeneDrug for MSI1

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 MSI1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0596263Carcinogenesis9BeFree
umls:C0017638Glioma5BeFree
umls:C0025149Medulloblastoma4BeFree,LHGDN
umls:C0007102Malignant tumor of colon3BeFree
umls:C0017636Glioblastoma3BeFree
umls:C0024623Malignant neoplasm of stomach3BeFree
umls:C0027627Neoplasm Metastasis3BeFree
umls:C0699790Colon Carcinoma3BeFree
umls:C0699791Stomach Carcinoma3BeFree
umls:C2239176Liver carcinoma3BeFree
umls:C0001418Adenocarcinoma2BeFree
umls:C0006142Malignant neoplasm of breast2BeFree
umls:C0027766Nervous System Neoplasms2BeFree
umls:C0242379Malignant neoplasm of lung2BeFree
umls:C0302592Cervix carcinoma2BeFree
umls:C0476089Endometrial Carcinoma2BeFree
umls:C0678222Breast Carcinoma2BeFree
umls:C0684249Carcinoma of lung2BeFree
umls:C0686619Secondary malignant neoplasm of lymph node2BeFree
umls:C0001430Adenoma1BeFree
umls:C0002395Alzheimer's Disease1LHGDN
umls:C0005684Malignant neoplasm of urinary bladder1BeFree
umls:C0006118Brain Neoplasms1BeFree
umls:C0007137Squamous cell carcinoma1BeFree
umls:C0007786Brain Ischemia1RGD
umls:C0007847Malignant tumor of cervix1BeFree
umls:C0009402Colorectal Carcinoma1BeFree
umls:C0014170Endometrial Neoplasms1LHGDN
umls:C0014175Endometriosis1BeFree
umls:C0019348Herpes Simplex Infections1BeFree
umls:C0023903Liver neoplasms1BeFree,LHGDN
umls:C0024117Chronic Obstructive Airway Disease1BeFree
umls:C0041327Tuberculosis, Pulmonary1BeFree
umls:C0178874Tumor Progression1BeFree
umls:C0206708Cervical Intraepithelial Neoplasia1BeFree
umls:C0236642Pick Disease of the Brain1LHGDN
umls:C0278803Adenocarcinoma of small intestine1BeFree
umls:C0279626Squamous cell carcinoma of esophagus1BeFree
umls:C0280100Solid tumour1BeFree
umls:C0338106Adenocarcinoma of colon1BeFree
umls:C0349458Cervical intraepithelial neoplasia grade 11BeFree
umls:C0349459Cervical intraepithelial neoplasia grade 21BeFree
umls:C0555198Malignant Glioma1BeFree
umls:C0699885Carcinoma of bladder1BeFree
umls:C0751955Brain Infarction1RGD
umls:C0948380Colorectal cancer metastatic1BeFree
umls:C1458155Mammary Neoplasms1BeFree
umls:C1527249Colorectal Cancer1BeFree
umls:C2987191Pancreatic Intraductal Papillary Mucinous Neoplasm, Gastric-Type1BeFree
umls:C3539878Triple Negative Breast Neoplasms1BeFree
umls:C3714514Infection1LHGDN