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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 LRWD1
check button Gene summary
Basic gene informationGene symbolLRWD1
Gene name
Synonyms
CytomapUCSC genome browser:
Type of gene
RefGenes
Description
Modification date
dbXrefs
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LRWD1
BioGPS: 100616367
PathwayNCI Pathway Interaction Database: LRWD1
KEGG: LRWD1
REACTOME: LRWD1
Pathway Commons: LRWD1
ContextiHOP: LRWD1
ligand binding site mutation search in PubMed: LRWD1
UCL Cancer Institute: LRWD1
Assigned class in TissGDB*A
Included tissue-specific gene expression resourcesHPA,TiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Testis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)TGCT
Reference showing the relevant tissue of LRWD1High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability. He T, Surdez D, Rantala JK, Haapa-Paananen S, Ban J, Kauer M, Tomazou E, Fey V, Alonso J, Kovar H, Delattre O, Iljin K. Gene. 2017 Jan 5;596:137-146. doi: 10.1016/j.gene.2016.10.021. Epub 2016 Oct 17. (pmid:27760381)
go to article
Description by TissGene annotationsTissgsLTS
* 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 LRWD1

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


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TissGene-miRNA for LRWD1

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 LRWD1
TissGeneSNV for LRWD1

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.A127VSTAD2
p.T600ILIHC1
p.E186KPAAD1
p.E94XKIRC1
p.E573KBLCA1
p.A86VPAAD1
p.L240RLIHC1
p.D53YHNSC1
p.A173TCOAD1
p.P102SSTAD1
p.E306DCESC1
p.P338LSKCM1
p.P302LLUSC1
p.K224RTHCA1
p.R234WCESC1
p.T410MCOAD1
p.A561VSTAD1
p.T630ASTAD1
p.D83NUCEC1
p.A642TPAAD1
p.D108NBLCA1
p.P181LSKCM1
p.R447CUCEC1
p.D53NBLCA1
p.S253LSKCM1
p.A634TCOAD1
p.N136KLAML1
p.L104MLGG1
p.D637YTHYM1
p.R124QBRCA1
p.A262TSTAD1
p.R533QSKCM1
p.V620MSKCM1
p.L419IUCEC1
p.S516RCOAD1
p.P102SSKCM1
p.V582IOV1
p.V271EKIRP1
p.I417SKIRP1
p.G67DSTAD1
p.R178SSTAD1
p.S55FLUSC1
p.E94*KIRC1
p.D83NTHYM1
p.P63LGBM1
p.A77TUCEC1
p.R447HLIHC1
p.E140KLUAD1
p.V582ICOAD1
p.R361HSTAD1
p.G465DSKCM1
p.A77TPRAD1
p.W524LKIRC1
p.K224RSKCM1
p.P593LCOAD1


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TissGeneCNV for LRWD1

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 LRWD1

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
Chimerdb3.0ChiTaRsNABG255749ELL3-LRWD1chr15:44087284chr7:102113562


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TissGeneNet for LRWD1

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)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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COAD (tumor)COAD (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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HNSC (tumor)HNSC (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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KICH (tumor)KICH (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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KIRC (tumor)KIRC (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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KIRP (tumor)KIRP (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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LIHC (tumor)LIHC (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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LUAD (tumor)LUAD (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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LUSC (tumor)LUSC (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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PRAD (tumor)PRAD (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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STAD (tumor)STAD (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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THCA (tumor)THCA (normal)
LRWD1, CUL4A, DDB1 (tumor)LRWD1, CUL4A, DDB1 (normal)
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TissGeneProg for LRWD1

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 LRWD1
TissGeneDrug for LRWD1

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 LRWD1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0376358Malignant neoplasm of prostate1BeFree
umls:C0600139Prostate carcinoma1BeFree