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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: ENSG00000261399

Summary for LA16c-329F2.1

check button Gene summary

Gene informationEnsembl ID

ENSG00000261399

Gene symbol

LA16c-329F2.1

Gene name
HGNC
Entrez ID
Gene typeantisense
Synonyms
UniProtAcc

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Structure and expression level for LA16c-329F2.1

check buttonDifferentially expressed gene analysis between cancer and normal samples.
DEG result
Ensembl IDBase meanlog2FC(AD/control)lfcSEStatP-valueAdjc.p-valueDEG direction Cancer type
ENSG000002613991.117129e+02-1.681975e+002.815289e-01-5.974430e+002.310000e-091.200000e-08DOWNTHCA
ENSG000002613998.537000e+01-2.231385e+002.932355e-01-7.609532e+002.750000e-141.160000e-13DOWNKIRC
ENSG000002613999.724882e+021.726768e+002.413987e-017.153179e+008.480000e-136.700000e-12UPKICH
ENSG000002613996.647120e+01-2.360100e+003.905015e-01-6.043766e+001.510000e-091.020000e-08DOWNKIRP
ENSG000002613992.064525e+012.281503e+003.888279e-015.867641e+004.420000e-092.510000e-08UPUCEC

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value
ENSG000002613994.603293e-015.655748e-06KICH1.269786e-05
ENSG00000261399-3.581581e-017.698072e-20KIRC5.773554e-19
ENSG00000261399-4.753485e-017.234444e-18KIRP6.314636e-16
ENSG00000261399-3.501537e-019.061283e-18THCA4.802480e-16

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lncRNA-Protein interaction for LA16c-329F2.1

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 LA16c-329F2.1

lncrna_DNA
check buttonlncRNA targets the enhancer region and positively regulates the gene expression.
Only predicted by TDF
TMEM38A,NDUFS3,C15orf61,TBC1D24,CYCS,MRPL34,TXNRD2,NECAB3,MKKS,ECI1,NDUFV1,UQCR11,GLRX5,UQCRC1,ILVBL,NHLRC4,NDUFA4,COQ3,MCRIP2,TMEM129
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 LA16c-329F2.1

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.
Only predicted by lncTar
ZYX,SFXN3,SH3GL1,BAZ1A
Exist in public source
NA

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 and exonskipping events negative correlated
LncRNA Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonLOF
ENSG00000261399ENST00000570022exon_skip_361434chr21:25997359-25997416-9.23-0.5429APPENST00000346798In-frame

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

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Variants for LA16c-329F2.1

check buttonRNA A-to-I editing events in lncRNA.
LncRNAediting IDLncRNA Ensembl IDChromosomeEditing PositionStrandGene TypeGene NameTranscript IDTranscript TypeTranscript Name

check buttonEdited-associated DElncRNAs in cancer.
LncRNA Ensembl IDLncRNA IndexCancer TypeChr_Postion_StrandAVE1AVE2log2FCW-valueP-valueAdjc.p-valueChange

check buttonCorrelation between RNA A-to-I editing events's frequecy and lncRNA expression.
LncRNA Ensembl IDLncRNA IndexCorrelationP-valueAdjc.p-value

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
ENSG00000261399ENSG00000010256UQCRC1DLBC,KICH,KIRC,KIRP,THCAKIRC
ENSG00000261399ENSG00000072954TMEM38ADLBC,KICH,KIRC,KIRP,THCAKICH
ENSG00000261399ENSG00000125863MKKSDLBC,KICH,KIRC,KIRP,THCAKICH
ENSG00000261399ENSG00000125967NECAB3DLBC,KICH,KIRC,THCA,UCECKICH
ENSG00000261399ENSG00000130312MRPL34DLBC,KICH,KIRC,KIRP,THCAKICH
ENSG00000261399ENSG00000132423COQ3DLBC,KICH,KIRC,KIRP,THCAKICH
ENSG00000261399ENSG00000162065TBC1D24DLBC,KICH,KIRC,KIRP,THCAKICHKIRC,KIRP
ENSG00000261399ENSG00000172115CYCSDLBC,KICH,KIRC,KIRP,THCAKICH
ENSG00000261399ENSG00000172366MCRIP2DLBC,KICH,KIRC,THCA,UCECKICH,UCEC
ENSG00000261399ENSG00000182512GLRX5DLBC,KICH,KIRC,KIRP,THCAKIRC
ENSG00000261399ENSG00000189043NDUFA4DLBC,KICH,KIRC,KIRP,THCAKICHKIRC
ENSG00000261399ENSG00000189227C15orf61DLBC,KICH,KIRC,KIRP,THCAKICH
ENSG00000261399ENSG00000257108NHLRC4DLBC,KIRC,KIRP,LAML,UCECKIRC,KIRP

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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
ENSG00000261399ENST00000570022SFXN3ENSG00000107819ENST00000489434-0.1015235THCA,KIRC-
ENSG00000261399ENST00000570022SH3GL1ENSG00000141985ENST00000417295-0.10261KIRC-
ENSG00000261399ENST00000570022ZYXENSG00000159840ENST00000436448-0.1695303KIRPUCEC
ENSG00000261399ENST00000570022BAZ1AENSG00000198604ENST00000556314-0.2131199KIRC,KIRP-

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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
ENSG00000261399.1ENST00000570022.176290520