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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 RMI1
check button Gene summary
Basic gene informationGene symbolRMI1
Gene nameRecQ mediated genome instability 1
SynonymsBLAP75|C9orf76|FAAP75
CytomapUCSC genome browser: 9q21.32
Type of geneprotein-coding
RefGenesNM_024945.2,
DescriptionBLM-associated polypeptide, 75 kDaBLM-associated protein 75 kDaRMI1, RecQ mediated genome instability 1, homologhomolog of yeast RecQ-mediated genome instability 1 (RMI1)recQ-mediated genome instability protein 1
Modification date20141207
dbXrefs MIM : 610404
HGNC : HGNC
Ensembl : ENSG00000178966
HPRD : 09867
Vega : OTTHUMG00000020113
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RMI1
BioGPS: 80010
PathwayNCI Pathway Interaction Database: RMI1
KEGG: RMI1
REACTOME: RMI1
Pathway Commons: RMI1
ContextiHOP: RMI1
ligand binding site mutation search in PubMed: RMI1
UCL Cancer Institute: RMI1
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)LiverTestis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LIHCTGCT
Reference showing the relevant tissue of RMI1
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 RMI1

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
BRCA1.3209011410.1673537731.1535473681.14E-362.31E-35
LUSC1.209843195-0.1902470011.4000901961.79E-151.18E-14
BLCA0.78542658-0.4055207891.1909473681.35E-050.00024375


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TissGene-miRNA for RMI1

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 RMI1
TissGeneSNV for RMI1

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.M613IESCA2
p.K166NREAD1
p.G525VESCA1
p.E614*ESCA1
p.R347QCOAD1
p.R62WLIHC1
p.P242SSKCM1
p.G148EBLCA1
p.T359MLGG1
p.P299TGBM1
p.E310*UCEC1
p.P163SSKCM1
p.T430APRAD1
p.W56LKIRC1
p.D587HREAD1
p.L168FACC1
p.Q457RBRCA1
p.T258IBLCA1
p.C366WSTAD1
p.D542YKIRP1
p.D71NBLCA1
p.S601YREAD1
p.K625TREAD1
p.D234NBRCA1
p.S174FSKCM1
p.L588VCOAD1
p.T430IPRAD1
p.L157IUCEC1
p.R395TCESC1
p.I173MTHCA1
p.V218ISKCM1
p.S477NSTAD1
p.D346NUCEC1
p.M561ISKCM1
p.L521VLUAD1
p.K419NCOAD1
p.G192SSKCM1
p.E37XCOAD1
p.N38KKIRC1
p.R347GLGG1
p.L236RLIHC1
p.K441RCESC1
p.D346NBLCA1
p.E614XESCA1
p.P356TBRCA1
p.H405YSKCM1
p.C464WSTAD1
p.L57FKIRC1
p.L339WSTAD1
p.F596CUCEC1
p.L43SCOAD1
p.A259TREAD1


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TissGeneCNV for RMI1

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 RMI1

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
TCGAfusionPortalPRADAGBMTCGA-06-0744-01ARMI1-STX17NAChr9:86595806Chr9:102691060


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TissGeneNet for RMI1

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)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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COAD (tumor)COAD (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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HNSC (tumor)HNSC (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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KICH (tumor)KICH (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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KIRC (tumor)KIRC (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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KIRP (tumor)KIRP (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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LIHC (tumor)LIHC (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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LUAD (tumor)LUAD (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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LUSC (tumor)LUSC (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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PRAD (tumor)PRAD (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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STAD (tumor)STAD (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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THCA (tumor)THCA (normal)
RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (tumor)RMI1, HNF4A, PFDN1, UBE3A, RPA1, BLM, FANCF, RPA2, FANCA, TOP3A, FANCM, NR1H2, APITD1, ERCC6L, HSPA13 (normal)
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TissGeneProg for RMI1

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 RMI1
TissGeneDrug for RMI1

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 RMI1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0005859Bloom Syndrome1GAD
umls:C0009402Colorectal Carcinoma1BeFree
umls:C0023467Leukemia, Myelocytic, Acute1BeFree,GAD,LHGDN
umls:C0025202melanoma1BeFree,GAD,LHGDN
umls:C0033027Preleukemia1GAD
umls:C0037286Skin Neoplasms1GAD
umls:C0376358Malignant neoplasm of prostate1GAD
umls:C0596263Carcinogenesis1BeFree
umls:C1332153Acute Myeloid Leukemia Arising from Previous Myelodysplastic Syndrome1BeFree
umls:C1527249Colorectal Cancer1BeFree,GAD
umls:C3463824MYELODYSPLASTIC SYNDROME1GAD