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Center for Computational Systems Medicine
Soverview

1. Gene summary of enriched editing regions

Soverview

2. Tumor-specific enriched editing regions

Comparison of enriched editing regions between tumor and normal.

Correlation of enriched editing regions with tumor stages.

Associations of enriched editing regions with cancer survival.

Soverview

3. Enriched editing regions and immune related genes

Soverview

4. Enriched editing regions and immune related splicing

Soverview

5. Enriched editing regions and immune infiltration

Soverview

6. Enriched editing regions and immune gene sets

Correlation of enriched editing regions with epithelial-mesenchymal transition.

Correlations of enriched editing regions with hypoxic.

Associations of enriched editing regions with hallmark gene sets from MSigDB.

Soverview

7. Enriched editing regions and drugs

Correlations between enriched editing regions and drug sensitivity.

Enriched editing regions targeted by drugs from DrugBank database.

Editing gene: KLHDC4 (ImmuneEditome ID:54758)

1. Gene summary of enriched editing regions for KLHDC4

check button Gene summary
Gene informationGene symbol

KLHDC4

Gene ID

54758

GeneSynonyms-
GeneCytomap

16q24.2

GeneTypeprotein-coding
GeneDescriptionkelch domain-containing protein 4
GeneModificationdate20230329
UniprotIDQ8TBB5;H3BUX8;Q9UF94;Q86VH3;H3BQH3;H3BQL0;H3BV82;H3BQ90;H3BP99;H3BTB1
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr16:87727954-87728836:-ENST00000316853.9ENSG00000104731.12KLHDC4ncRNA_intronicAluSz6,AluSgchr16:87727954-87728836:-.alignment
chr16:87727954-87728836:-ENST00000562872.1ENSG00000104731.12KLHDC4ncRNA_intronicAluSz6,AluSgchr16:87727954-87728836:-.alignment
chr16:87727954-87728836:-ENST00000564484.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSz6,AluSgchr16:87727954-87728836:-.alignment
chr16:87727954-87728836:-ENST00000566349.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSz6,AluSgchr16:87727954-87728836:-.alignment
chr16:87727954-87728836:-ENST00000566661.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSz6,AluSgchr16:87727954-87728836:-.alignment
chr16:87727954-87728836:-ENST00000567513.1ENSG00000104731.12KLHDC4ncRNA_intronicAluSz6,AluSgchr16:87727954-87728836:-.alignment
chr16:87731099-87732372:-ENST00000316853.9ENSG00000104731.12KLHDC4ncRNA_intronicAluSq,L1ME1,AluSzchr16:87731099-87732372:-.alignment
chr16:87731099-87732372:-ENST00000564484.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSq,L1ME1,AluSzchr16:87731099-87732372:-.alignment
chr16:87731099-87732372:-ENST00000565328.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSq,L1ME1,AluSzchr16:87731099-87732372:-.alignment
chr16:87731099-87732372:-ENST00000566349.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSq,L1ME1,AluSzchr16:87731099-87732372:-.alignment
chr16:87731099-87732372:-ENST00000566661.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSq,L1ME1,AluSzchr16:87731099-87732372:-.alignment
chr16:87731099-87732372:-ENST00000567513.1ENSG00000104731.12KLHDC4ncRNA_intronicAluSq,L1ME1,AluSzchr16:87731099-87732372:-.alignment
chr16:87737373-87737913:-ENST00000316853.9ENSG00000104731.12KLHDC4ncRNA_intronicAluSx1,AluSzchr16:87737373-87737913:-.alignment
chr16:87737373-87737913:-ENST00000564484.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSx1,AluSzchr16:87737373-87737913:-.alignment
chr16:87737373-87737913:-ENST00000565328.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSx1,AluSzchr16:87737373-87737913:-.alignment
chr16:87737373-87737913:-ENST00000566349.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSx1,AluSzchr16:87737373-87737913:-.alignment
chr16:87737373-87737913:-ENST00000566661.4ENSG00000104731.12KLHDC4ncRNA_intronicAluSx1,AluSzchr16:87737373-87737913:-.alignment
chr16:87737373-87737913:-ENST00000567513.1ENSG00000104731.12KLHDC4ncRNA_intronicAluSx1,AluSzchr16:87737373-87737913:-.alignment


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2. Tumor-specific enriched editing regions for KLHDC4


all structure

check buttonComparison of enriched editing regions between tumor and normal.
* P<0.05 and Informative number >=20.
* EER: enriched editing region, EAG: EER-associated genes.
ID_eventscancerTypePBoxplot


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check buttonCorrelation of enriched editing regions with tumor stages.
* AnovaP<0.05, Pearson P<0.05 and Informative number >=20.
* EER: enriched editing region, EAG: EER-associated genes, Path: Pathological stage, Cli: Clinical stage.
* Only shows the most significant correlation result of EERs/EAGs with either pathological stage or clinical stage according to correlation coefficient (R). For more results, please go to download page.
ID_eventscancerTypeStageTypeAnovaPPRBoxplot
chr16:87731099-87732372:-BLCAPathEER3.8742e-022.9578e-020.4270image


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check button Associations of enriched editing regions with cancer survival.
* Pkm<0.05 and Pcox<0.05.
* EER: enriched editing region, EAG: EER-associated genes.
ID_eventscancerTypeIDPkmPcox_continuousHR_continuousKMPlot

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3. Enriched editing regions and immune related genes for KLHDC4


all structure

check button Enriched editing regions and immune related genes.
* First, the associations between enriched editing regions and genes were tested by QTL and Pearson method (QTL: FDR<0.05 and Pearson: P<0.05).
* Second, the gene relationships with immune were tested by three analyses: whether the gene is an immune gene (InnateDB、Immport、Immunome、Immunogenetic Related Information Source (IRIS)), whether the gene is associated with immune infiltration and whether the gene is related to immune gene sets.
* EER: enriched editing region, EAG: EER-associated genes.
* Only shows the most significant correlation result of genes with the fraction of different immune cells and the scores of 50 hallmark genesets according to correlation coefficient (R). For more results, please go to download page.
ID_eventscancerTypeGenebetaFDRPearsonPPearsonRCorrelationPlotRBPRBPtargetsImmuneGeneImmuneFractionHallMark

More results



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4. Enriched editing regions and immune related splicing for KLHDC4


all structure

check button Enriched editing regions and immune related splicing.
* First, the associations between enriched editing regions and splicing events were tested by QTL and Pearson method (QTL: FDR<0.05 and Pearson: P<0.05).
* Second, the splicing relationships with immune were tested by three analyses: whether the splicing event locates in an immune gene (InnateDB、Immport, Immunome and Immunogenetic Related Information Source (IRIS)), whether the splicing event is associated with immune infiltration and whether the splicing event is related to immune gene sets.
* EER: enriched editing region, EAG: EER-associated genes.
* Only shows the most significant correlation result of splicing events with the fraction of different immune cells and the scores of 50 hallmark genesets according to correlation coefficient (R). For more results, please go to download page.
ID_eventscancerTypeSplicingTypeSplicingGeneSplicingChrSplicingPositionbetaFDRPearsonPPearsonRCorrelationPlotRBPRBPtargetsImmuneGeneImmuneFractionHallMark

More results



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5. Enriched editing regions and immune infiltration for KLHDC4


all structure

check button Associations of enriched editing regions with immune infiltration.
* P<0.05 and Informative number >=20.
* EER: enriched editing region, EAG: EER-associated genes.
* Only shows the most significant correlation result of EERs/EAGs with the fraction of different immune cells according to correlation coefficient (R). For more results, please go to download page.
ID_eventscancerTypeIDImmuneCellPRCorrelationPlot
chr16:87731099-87732372:-BLCAEERDendritic_cells_resting7.5662e-03-0.5115image
ENSG00000104731.12,KLHDC4BLCAEAGDendritic_cells_resting2.4098e-02-0.4179image
chr16:87731099-87732372:-BRCAEERNK_cells_resting1.3795e-020.4859image
chr16:87731099-87732372:-ESCAEERB_cells_naive4.6694e-03-0.3041image
ENSG00000104731.12,KLHDC4ESCAEAGEosinophils7.0196e-060.4494image
chr16:87731099-87732372:-LAMLEERDendritic_cells_activated2.6528e-020.4265image
ENSG00000104731.12,KLHDC4LAMLEAGT_cells_CD4_memory_resting1.4523e-020.3090image
ENSG00000104731.12,KLHDC4LUSCEAGDendritic_cells_resting3.9664e-02-0.4226image
chr16:87731099-87732372:-OVEERNeutrophils1.4124e-030.4523image
ENSG00000104731.12,KLHDC4OVEAGNeutrophils1.7668e-030.4233image
ENSG00000104731.12,KLHDC4PRADEAGEosinophils6.2358e-050.7134image
chr16:87737373-87737913:-STADEERDendritic_cells_activated3.0022e-020.3238image
ENSG00000104731.12,KLHDC4STADEAGT_cells_regulatory_(Tregs)3.9933e-02-0.1685image


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6. Enriched editing regions and immune gene sets for KLHDC4


all structure

check button Correlation of enriched editing regions with epithelial-mesenchymal transition.
* First, the differences of enriched editing regions between Epi and Mes groups (defined by KS-test) were compared (P<0.05 and Informative number >=20).
* Second, the correlations between enriched editing regions and gene set score of HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION were analyzed (P<0.05 and Informative number >=20).
* EER: enriched editing region, EAG: EER-associated genes.
* Only shows the EERs/EAGs significantly edited between Epi and Mes group.
ID_eventscancerTypeE2M_PBoxplotCorPCorRCorrelationPlot


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check button Correlations of enriched editing regions with hypoxic.
* First, there are four hypoxia scores used in the database. The first three hypoxic scores were calculated on three gene sets of Buffa, Ragnum and Winter based on one previous study (PMID: 32024819). One last hypoxia score was defined on HALLMARK_HYPOXIA by GSVA method.
* Second, the correlations enriched editing regions with the four hypoxic scores were analyzed (P<0.05 and Informative number >=20).
* EER: enriched editing region, EAG: EER-associated genes.
* Only shows the EERs/EAGs significantly correlated with all four hypoxia gene set scores. For more results, please go to download page.
ID_eventscancerTypeBuffa_P Buffa_R Ragnum_P Ragnum_R Winter_P Winter_R HALLMARK_P HALLMARK_R CorrelationPlot


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check button Associations of enriched editing regions with hallmark gene sets from MSigDB.
* P<0.05 and Informative number >=20.
* EER: enriched editing region, EAG: EER-associated genes.
* Only shows the most significant correlation result of EERs/EAGs with the scores of 50 hallmark genesets according to correlation coefficient (R). For more results, please go to download page.
ID_eventscancerHallmarkTypeTypePRCorrelationPlot
chr16:87731099-87732372:-BLCAGSVA_HALLMARK_XENOBIOTIC_METABOLISMEER2.6557e-040.6571image
ENSG00000104731.12,KLHDC4BLCAGSVA_HALLMARK_ADIPOGENESISEAG1.9607e-020.4309image
ENSG00000104731.12,KLHDC4BRCAGSVA_HALLMARK_ANDROGEN_RESPONSEEAG2.2276e-030.5288image
ENSG00000104731.12,KLHDC4COADGSVA_HALLMARK_KRAS_SIGNALING_UPEAG8.5887e-040.6586image
chr16:87731099-87732372:-ESCAGSVA_HALLMARK_NOTCH_SIGNALINGEER1.6843e-030.3357image
ENSG00000104731.12,KLHDC4ESCAGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG2.3617e-020.2358image
ENSG00000104731.12,KLHDC4KIRCGSVA_HALLMARK_KRAS_SIGNALING_DNEAG3.9211e-02-0.4067image
ENSG00000104731.12,KLHDC4LAMLGSVA_HALLMARK_PROTEIN_SECRETIONEAG2.6282e-020.2822image
chr16:87731099-87732372:-LAMLGSVA_HALLMARK_BILE_ACID_METABOLISMEER3.5502e-02-0.4062image
ENSG00000104731.12,KLHDC4LUSCGSVA_HALLMARK_E2F_TARGETSEAG2.1795e-02-0.4658image
chr16:87731099-87732372:-OVGSVA_HALLMARK_NOTCH_SIGNALINGEER1.0951e-020.3679image
ENSG00000104731.12,KLHDC4OVGSVA_HALLMARK_NOTCH_SIGNALINGEAG9.1597e-030.3580image
chr16:87737373-87737913:-STADGSVA_HALLMARK_ESTROGEN_RESPONSE_EARLYEER2.1764e-020.3413image


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7. Enriched editing regions and drugs for KLHDC4


all structure

check button Correlations between enriched editing regions and drug sensitivity.
* First, the drug sensitivity (IS50) was estimated on 84 drugs by pRRophetic package.
* Second, the correlations between editing enriched regions and drug sensitivity were analyzed (P<0.05 and Informative number >=20).
* EER: enriched editing region, EAG: EER-associated genes.
* Only shows the most significant correlation result of EERs/EAGs with the IS50 scores of 84 drugs according to correlation coefficient (R). For more results, please go to download page.
ID_eventscancerDrugTypePRCorrelationPlot
chr16:87731099-87732372:-BLCABIRB.0796EER3.0880e-040.6518image
ENSG00000104731.12,KLHDC4BLCABIRB.0796EAG6.9798e-040.5930image
chr16:87731099-87732372:-BRCABMS.536924EER2.4283e-020.4492image
ENSG00000104731.12,KLHDC4BRCAFH535EAG1.4331e-03-0.5475image
ENSG00000104731.12,KLHDC4COADDMOGEAG2.1100e-03-0.6194image
chr16:87731099-87732372:-ESCABexaroteneEER6.4536e-03-0.2932image
chr16:87737373-87737913:-ESCALapatinibEER5.5546e-03-0.5101image
ENSG00000104731.12,KLHDC4ESCAEHT.1864EAG1.6596e-020.2492image
ENSG00000104731.12,KLHDC4KIRCBosutinibEAG4.9775e-030.5338image
ENSG00000104731.12,KLHDC4LAMLImatinibEAG5.2115e-03-0.3506image
chr16:87731099-87732372:-LAMLKIN001.135EER4.2645e-020.3929image
ENSG00000104731.12,KLHDC4LUADLFM.A13EAG1.7815e-030.4530image
ENSG00000104731.12,KLHDC4LUSCLFM.A13EAG7.2417e-03-0.5336image
chr16:87731099-87732372:-OVBleomycinEER9.1311e-03-0.3763image
ENSG00000104731.12,KLHDC4OVBleomycinEAG2.0189e-02-0.3213image
ENSG00000104731.12,KLHDC4PRADBAY.61.3606EAG8.0050e-03-0.5179image
chr16:87737373-87737913:-STADCCT018159EER6.0698e-03-0.4029image
ENSG00000104731.12,KLHDC4STADCGP.60474EAG1.7047e-03-0.2549image
chr16:87731099-87732372:-STADCytarabineEER8.7704e-030.2290image


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check button EAGs targeted by drugs from DrugBank database.
* EAG: EER-associated genes.
EERENSTUniprotIDDrugBankIDDrugDrugType