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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 SLIT1
check button Gene summary
Basic gene informationGene symbolSLIT1
Gene nameslit homolog 1 (Drosophila)
SynonymsMEGF4|SLIL1|SLIT-1|SLIT3
CytomapUCSC genome browser: 10q23.3-q24
Type of geneprotein-coding
RefGenesNM_003061.2,
Descriptionmultiple EGF-like domains protein 4multiple epidermal growth factor-like domains protein 4slit homolog 1 protein
Modification date20141207
dbXrefs MIM : 603742
HGNC : HGNC
Ensembl : ENSG00000187122
HPRD : 04773
Vega : OTTHUMG00000018843
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SLIT1
BioGPS: 6585
PathwayNCI Pathway Interaction Database: SLIT1
KEGG: SLIT1
REACTOME: SLIT1
Pathway Commons: SLIT1
ContextiHOP: SLIT1
ligand binding site mutation search in PubMed: SLIT1
UCL Cancer Institute: SLIT1
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesHPA,TiGER
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Brain
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)GBM,LGG
Reference showing the relevant tissue of SLIT1
Description by TissGene annotationsProtective TissGene in RFS
Fused withOncogene
Fused withTSGene
* 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
GO:0007411axon guidance11748139
GO:0021834chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration11748139
GO:0048846axon extension involved in axon guidance16840550
GO:0050919negative chemotaxis11748139
GO:0007411axon guidance11748139
GO:0021834chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration11748139
GO:0048846axon extension involved in axon guidance16840550
GO:0050919negative chemotaxis11748139


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TissGeneExp for SLIT1

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
THCA3.729448134-1.6268654265.3563135591.30E-228.47E-21
PRAD2.737078642-0.5797213583.31681.31E-184.89E-16
STAD-2.524046358-1.474646358-1.04940.002140.009606507
KIRP-2.205952608-3.2567776081.0508250.001350.003586137
COAD-2.348559819-1.237521358-1.1110384620.0009370.002701272
LUSC-1.838915475-0.706848809-1.1320666677.82E-050.000164125


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TissGene-miRNA for SLIT1

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
LUADhsa-miR-340-5pMIMAT00046920.028-0.2960


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TissGeneMut for SLIT1
TissGeneSNV for SLIT1

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.R1460LLUAD2
p.V1258MSKCM2
p.G850DSKCM2
p.G683VBLCA1
p.R1481CCOAD1
p.R88WLIHC1
p.E1282KCOAD1
p.R1481HCOAD1
p.Y381CTHCA1
p.A1440VLGG1
p.V1470AUCS1
p.R374HUCEC1
p.V1292MPRAD1
p.R1439HPRAD1
p.C1497YSTAD1
p.A1058VREAD1
p.R1300HBLCA1
p.G478ESKCM1
p.V511MLUAD1
p.L920MESCA1
p.R537HCOAD1
p.G1139VCOAD1
p.R15WCOAD1
p.D1514YLUAD1
p.Q1137HLIHC1
p.H941DPCPG1
p.F441YSKCM1
p.D294GESCA1
p.L1279ICOAD1
p.N1169KCOAD1
p.E1119DLGG1
p.P933QLUAD1
p.N79SLGG1
p.N474KLUAD1
p.G1095RSKCM1
p.S1233FSKCM1
p.L920MLUAD1
p.Q163EOV1
p.N936SLUSC1
p.A1234TLGG1
p.P1073TLUAD1
p.L1285RSKCM1
p.G1416RPAAD1
p.N161HUCS1
p.R605QSKCM1
p.E101KSKCM1
p.F329ILUAD1
p.S1281NSKCM1
p.G42AKIRC1
p.R637CSTAD1
p.N474ILUSC1
p.L839IREAD1
p.R835HCOAD1
p.P708SSKCM1
p.G559VLUAD1
p.H213QHNSC1
p.G559WLUAD1
p.E551QBLCA1
p.C1533FMESO1
p.G655ESKCM1
p.T1240MPAAD1
p.L364FSKCM1
p.R1091HUCEC1
p.A1440VLIHC1
p.E974KSKCM1
p.G175VPRAD1
p.D1078NHNSC1
p.E184DLGG1
p.S411PPAAD1
p.P918SSKCM1
p.Q1178KACC1
p.L1323QLIHC1
p.Q706HBLCA1
p.T1480MPRAD1
p.E491*UCEC1
p.R1187WLIHC1
p.L180VBLCA1
p.K484TPAAD1
p.N319SCOAD1
p.H77YLGG1
p.D1226NSKCM1
p.P701AOV1
p.L663FSKCM1
p.E260KCESC1
p.A179VUCEC1
p.P325SSKCM1
p.G694RLUAD1
p.E1322KCOAD1
p.G559VUCEC1
p.C286FLUAD1
p.D1462NTHYM1
p.R429WPAAD1
p.R118QSKCM1
p.K1164ECOAD1
p.F401LBRCA1
p.L412QSTAD1
p.R181WLGG1
p.Q1137HBLCA1
p.S1449LSKCM1
p.P735SACC1
p.T1196MSTAD1
p.P373SSKCM1
p.N794HBLCA1
p.L775MSARC1
p.P1155LMESO1
p.I145MLUSC1
p.V639IUCEC1
p.G587SSKCM1
p.G1146CCOAD1
p.D399NSKCM1
p.R233GLUSC1
p.N623KHNSC1
p.G375DKIRC1
p.E1322KHNSC1
p.P760LSKCM1
p.N1026IOV1
p.A713TCOAD1
p.A1197TKIRC1
p.R1439HUCEC1
p.R455HUCEC1
p.G1244VSTAD1
p.R178HSARC1
p.A1213TUCEC1
p.D943NSKCM1
p.G98VHNSC1
p.E1451KREAD1
p.A473TUCEC1
p.D1172NSKCM1
p.F177COV1
p.G1133RLUSC1
p.Q1030RSTAD1
p.S857FSKCM1
p.E1365KUCEC1
p.H873YBLCA1
p.E317KSKCM1
p.P514SSKCM1
p.R181WCOAD1
p.R1502QPAAD1
p.Q1353LLUAD1
p.D646NSKCM1
p.R835CCOAD1
p.L1203IESCA1
p.G1133VLUAD1
p.A437EESCA1
p.K563TUCEC1
p.R1187WCOAD1
p.E721KSKCM1
p.R687WUCEC1
p.A451THNSC1
p.G49CKIRP1
p.A1213TBLCA1
p.G267ESKCM1
p.G694RSKCM1
p.R357HLGG1
p.G1379SLIHC1
p.R465HESCA1
p.D510YLUAD1
p.R637HUCEC1
p.N575SSTAD1
p.A82VCOAD1
p.S1048CCESC1
p.D220NCOAD1
p.A473THNSC1
p.C519*LUAD1
p.Q133HLUAD1


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TissGeneCNV for SLIT1

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 SLIT1

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
Chimerdb3.0ChiTaRsNABM676949SLIT1-FAM208Bchr10:98758125chr10:5789503
Chimerdb3.0ChiTaRsNABF934573SLIT1-RAB10chr10:98850810chr2:26357905
Chimerdb3.0FusionScanBRCATCGA-A7-A6VV-01ATM9SF3-SLIT1Out-of-Framechr10:98346490chr10:98808875
TCGAfusionPortalPRADABRCATCGA-A7-A6VV-01ATM9SF3-SLIT1Out-of-frameChr10:98346491Chr10:98808875
TCGAfusionPortalPRADAGBMTCGA-12-5299-01ASLIT1-SFRP5Out-of-frameChr10:98790514Chr10:99527617


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TissGeneNet for SLIT1

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)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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COAD (tumor)COAD (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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HNSC (tumor)HNSC (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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KICH (tumor)KICH (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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KIRC (tumor)KIRC (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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KIRP (tumor)KIRP (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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LIHC (tumor)LIHC (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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LUAD (tumor)LUAD (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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LUSC (tumor)LUSC (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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PRAD (tumor)PRAD (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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STAD (tumor)STAD (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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THCA (tumor)THCA (normal)
SLIT1, ATN1, ROBO1, GPC1 (tumor)SLIT1, ATN1, ROBO1, GPC1 (normal)
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TissGeneProg for SLIT1

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 SLIT1
TissGeneDrug for SLIT1

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 SLIT1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0024623Malignant neoplasm of stomach2BeFree
umls:C0699791Stomach Carcinoma2BeFree
umls:C1527249Colorectal Cancer2BeFree
umls:C0003873Rheumatoid Arthritis1BeFree
umls:C0006111Brain Diseases1GAD
umls:C0006142Malignant neoplasm of breast1BeFree
umls:C0007115Malignant neoplasm of thyroid1BeFree
umls:C0014175Endometriosis1BeFree
umls:C0017638Glioma1BeFree
umls:C0019270Hernia1BeFree
umls:C0036341Schizophrenia1BeFree
umls:C0242379Malignant neoplasm of lung1BeFree
umls:C0346429Multiple malignancy1BeFree
umls:C0428886Mean blood pressure1GWASCAT
umls:C0549473Thyroid carcinoma1BeFree
umls:C0596263Carcinogenesis1BeFree
umls:C0678222Breast Carcinoma1BeFree
umls:C0684249Carcinoma of lung1BeFree
umls:C1302401Adenoma of large intestine1BeFree
umls:C1458155Mammary Neoplasms1LHGDN
umls:C1519670Tumor Angiogenesis1BeFree