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Center for Computational Systems Medicine
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lncRNA summary

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lncRNA structure and expression level

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lncRNA-Protein interaction

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lncRNA-DNA interaction

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lncRNA-RNA interaction

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Variants in lncRNA

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lncRNAs regulate the target genes through functioning as enhancers

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lncRNAs regulate the target genes through recruiting transcript factors

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lncRNAs regulate the alternative splicing events through interacting with splicing factor

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lncRNAs regulate mRNA through targeting the 3'-UTR region

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lncRNAs regulate mRNA by competing with miRNA

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lncRNA coding potential

lncRNA: ENSG00000173727

Summary for CMB9-22P13.1

check button Gene summary

Gene informationEnsembl ID

ENSG00000173727

Gene symbol

CMB9-22P13.1

Gene name
HGNC
Entrez ID
Gene typelincRNA
Synonyms
UniProtAcc

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Structure and expression level for CMB9-22P13.1

check buttonAS events and RNA A-to-I editing events of lncRNA in TCGA based on Genvode V22 structure.
UCSC result

check buttonDifferentially expressed gene analysis between cancer and normal samples.
DEG result
Ensembl IDBase meanlog2FC(AD/control)lfcSEStatP-valueAdjc.p-valueDEG direction Cancer type
ENSG000001737272.160773e+021.882338e+004.219387e-014.461164e+008.150000e-065.350000e-05UPGBM
ENSG000001737272.271162e+021.712012e+001.223984e-011.398721e+011.870000e-443.600000e-43UPKIRC
ENSG000001737272.415798e+021.134581e+001.791378e-016.333566e+002.400000e-101.800000e-09UPHNSC
ENSG000001737272.490165e+021.429336e+003.976442e-013.594509e+003.250040e-043.275181e-03UPESCA
ENSG000001737273.173054e+022.558479e+001.706357e-011.499381e+018.060000e-512.000000e-49UPLUSC
ENSG000001737272.080164e+022.287738e+001.794343e-011.274973e+013.130000e-379.180000e-36UPLUAD
ENSG000001737278.701265e+012.599091e+002.664683e-019.753843e+001.780000e-224.320000e-21UPLIHC

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value
ENSG000001737273.942807e-014.756401e-24KIRC6.794858e-23
ENSG000001737274.253540e-015.242008e-19LIHC3.636643e-17
ENSG00000173727-3.273050e-011.341087e-15THCA3.046183e-14

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lncRNA-Protein interaction for CMB9-22P13.1

lncrna_protein
check buttonlncRNA-epigenetic factor interaction (#cancer types with positive correlation >= 5).
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source

check buttonlncRNA-transcript factor interaction (#cancer types with positive correlation >= 5).
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source

check buttonlncRNA-RNA binding protein interaction (#cancer types with positive correlation >= 5).
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source

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lncRNA-DNA interaction for CMB9-22P13.1

lncrna_DNA
check buttonlncRNA targets the enhancer region and positively regulates the gene expression.
Only predicted by TDF
DDX55,SOX12,USF1
Exist in public source
NA

check buttonlncRNA targets the promoter region and positively regulates the gene expression.

check buttonlncRNA targets the promoter region and negatively regulates the gene expression.

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lncRNA-RNA interaction for CMB9-22P13.1

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.

check buttonlncRNA targets the skipped exon region.
-lncRNA and exonskipping events are positively correlated.
LncRNA Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonORF mutation

-lncRNA and exonskipping events are negatively correlated.
LncRNA Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonLOF

check buttonlncRNA targets by miRNA.
LncRNA Ensembl IDmiRNA IDLncRNA ENST IDBinding site in lncRNAScoreEnergyAlign LenPublic source

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Variants for CMB9-22P13.1

check buttonRNA A-to-I editing events in lncRNA.
LncRNAediting IDLncRNA Ensembl IDChromosomeEditing PositionStrandGene TypeGene NameTranscript IDTranscript TypeTranscript Name
LncEditing_243353ENSG00000173727.10chr1165457074+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243461ENSG00000173727.10chr1165459243+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243464ENSG00000173727.10chr1165459879+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243488ENSG00000173727.10chr1165460052+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243506ENSG00000173727.10chr1165460453+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243518ENSG00000173727.10chr1165460533+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243525ENSG00000173727.10chr1165460594+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243530ENSG00000173727.10chr1165460620+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243531ENSG00000173727.10chr1165460621+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243582ENSG00000173727.10chr1165461486+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243587ENSG00000173727.10chr1165461536+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243597ENSG00000173727.10chr1165461632+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243598ENSG00000173727.10chr1165461646+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243650ENSG00000173727.10chr1165462686+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243720ENSG00000173727.10chr1165463541+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243726ENSG00000173727.10chr1165463581+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243739ENSG00000173727.10chr1165463799+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243753ENSG00000173727.10chr1165463936+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243815ENSG00000173727.10chr1165464753+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243856ENSG00000173727.10chr1165465727+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243857ENSG00000173727.10chr1165465736+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002
LncEditing_243861ENSG00000173727.10chr1165466646+lincRNACMB9-22P13.1ENST00000309775.8lincRNACMB9-22P13.1-002

check buttonEdited-associated DElncRNAs in cancer.
Differentially expressed gene
LncRNA Ensembl IDLncRNA IndexCancer TypeChr_Postion_StrandAVE1AVE2log2FCW-valueP-valueAdjc.p-valueChange
ENSG00000173727LncEditing_243753UCSchr11_65463936_+1.018348e+014.571909e+008.655290e-013.019934e+002.528300e-034.558232e-03UP
ENSG00000173727LncEditing_243353OVchr11_65457074_+1.102145e+014.872850e+008.492737e-017.858750e+003.879843e-151.101085e-14UP
ENSG00000173727LncEditing_243461OVchr11_65459243_+9.982009e+005.195964e+001.061640e+005.982027e+002.203782e-093.518017e-09UP
ENSG00000173727LncEditing_243464OVchr11_65459879_+1.102607e+014.637694e+008.003591e-018.577233e+009.718243e-183.525019e-17UP
ENSG00000173727LncEditing_243488OVchr11_65460052_+1.164901e+014.939131e+008.078340e-017.437298e+001.027653e-132.519805e-13UP
ENSG00000173727LncEditing_243518OVchr11_65460533_+1.089045e+015.105572e+009.149813e-016.721693e+001.796248e-113.510233e-11UP
ENSG00000173727LncEditing_243525OVchr11_65460594_+1.111274e+014.761499e+008.178441e-018.295134e+001.084629e-163.505507e-16UP
ENSG00000173727LncEditing_243530OVchr11_65460620_+1.024479e+015.179850e+001.016354e+006.864066e+006.692770e-121.363013e-11UP
ENSG00000173727LncEditing_243531OVchr11_65460621_+1.094099e+014.922212e+008.677812e-017.803928e+006.000944e-151.654533e-14UP
ENSG00000173727LncEditing_243582OVchr11_65461486_+9.621609e+004.405229e+008.872633e-019.564039e+001.132483e-215.933436e-21UP
ENSG00000173727LncEditing_243587OVchr11_65461536_+1.092936e+014.716210e+008.247363e-018.366831e+005.918858e-171.961221e-16UP
ENSG00000173727LncEditing_243597OVchr11_65461632_+9.756457e+004.204194e+008.233651e-011.043122e+011.785892e-251.346007e-24UP
ENSG00000173727LncEditing_243598OVchr11_65461646_+1.000588e+014.434967e+008.518953e-019.570241e+001.066572e-215.604074e-21UP
ENSG00000173727LncEditing_243650OVchr11_65462686_+9.439346e+005.247784e+001.180667e+005.685019e+001.307983e-081.966787e-08UP
ENSG00000173727LncEditing_243720OVchr11_65463541_+8.738266e+004.273098e+009.689315e-019.929536e+003.096945e-231.843134e-22UP
ENSG00000173727LncEditing_243726OVchr11_65463581_+9.897256e+004.782267e+009.529856e-017.825221e+005.067655e-151.416325e-14UP
ENSG00000173727LncEditing_243739OVchr11_65463799_+9.925871e+004.224217e+008.113526e-011.076548e+015.010027e-274.345962e-26UP
ENSG00000173727LncEditing_243753OVchr11_65463936_+1.020450e+014.750062e+009.064649e-018.694881e+003.471924e-181.319187e-17UP
ENSG00000173727LncEditing_243815OVchr11_65464753_+1.076873e+015.069135e+009.199322e-017.078976e+001.452233e-123.186942e-12UP
ENSG00000173727LncEditing_243856OVchr11_65465727_+1.118000e+014.999332e+008.612429e-017.939889e+002.023629e-155.796656e-15UP
ENSG00000173727LncEditing_243857OVchr11_65465736_+9.894225e+005.003790e+001.016709e+007.147291e+008.850729e-131.980108e-12UP
ENSG00000173727LncEditing_243861OVchr11_65466646_+1.087878e+014.821000e+008.517068e-017.953393e+001.814710e-155.237945e-15UP

check buttonCorrelation between RNA A-to-I editing events's frequecy and lncRNA expression.
LncRNA Ensembl IDLncRNA IndexCorrelationP-valueAdjc.p-value
ENSG00000173727LncEditing_243739-8.703368e-011.083034e-024.053935e-02
ENSG00000173727LncEditing_243506-4.659359e-013.656259e-035.600856e-03
ENSG00000173727LncEditing_243587-3.152875e-011.413671e-021.615419e-02

check buttonCis-expression quantitative trait loci(cis-eQTL) of lncRNA.
LncRNA Ensembl IDLncRNA NameSNP infoNumber of Positive corelated CancerPositive corelated CancerNumber of Negative corelated CancerNegative corelated Cancer

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lncRNAs regulate the target genes through functioning as enhancers

lncrna_enhancer
check buttonlncRNA regulates differentially expressed genes by function as enhancer.
LncRNA Ensembl IDPC Gene IDPC Gene NamePositive correlated cancersCancer with PC gene up-regulationCancer with PC gene down-regulation

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lncRNAs regulate the target genes through recruiting transcript factors

lncrna_TF
check buttonLncRNA-TF complex positively regulates the gene expression by target promoter region (#cancer types with positive correlation >= 5).
lncRNA IDTF IDTF NamePCgene IDPCgene NameNumber of CancerCanaer Types

check buttonLncRNA-TF complex negatively regulates the gene expression by target promoter region (#cancer types with negative correlation >= 5).
lncRNA IDTF IDTF NamePCgene IDPCgene NameNumber of CancerCanaer Types

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lncRNAs regulate the alternative splicing event through interacting with splicing factor

lncrna_AS
check buttonLncRNA-RBP complex positively regulates the exon skippping events by target skipped eoxon region.
LncRNA Ensembl IDRBP IDRBP Gene NameExon Skipping IDSkipped ExonEX Gene NameEX Affected TransIDORF_annoCancer Type

check buttonLncRNA-RBP complex negatively regulates the exon skippping events by target skipped eoxon region.
LncRNA Ensembl IDRBP IDRBP Gene NameExon Skipping IDSkipped ExonEX Gene NameEX Affected TransIDORF_annoCancer Type

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lncRNAs regulate mRNA through targeting the 3'-UTR region

lncrna_mRNA
check buttonlncRNA regulates differential expressed mRNA by directly targeting 3' UTR region.
LncRNA Ensembl IDLncRNA ENST IDPC Gene NamePC Gene IDPC ENST IDdGnDGCancer with PC gene up-regulationCancer with PC gene Down-regulation

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lncRNAs regulate mRNA by competing with miRNA

lncrna_miRNA
check buttonlncRNA regulates mRNA by competing the miRNA binding site with mRNA.
LncRNA Ensembl IDlncRNA-miRNA-mRNACancer Types

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lncRNA coding potential

check buttonORFfinder result for the gencode.v22.lncRNA.transcript.fa.
lncRNA Ensembl IDlncRNA ENST IDlength(AA)start at transcriptend at transcript
ENSG00000173727.10ENST00000619960.335408301
ENSG00000173727.10ENST00000309775.8110742410