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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: PPM1K (ImmuneEditome ID:152926)

1. Gene summary of enriched editing regions for PPM1K

check button Gene summary
Gene informationGene symbol

PPM1K

Gene ID

152926

GeneSynonymsBDP|MSUDMV|PP2Ckappa|PP2Cm|PTMP|UG0882E07
GeneCytomap

4q22.1

GeneTypeprotein-coding
GeneDescriptionprotein phosphatase 1K, mitochondrial|PP2C domain-containing protein phosphatase 1K|PP2C-kappa|PP2C-type mitochondrial phosphoprotein phosphatase|branched-chain I+/--ketoacid dehydrogenase phosphatase|branched-chain alpha-ketoacid dehydrogenase phosphatase|protein phosphatase 2C kappa
GeneModificationdate20230518
UniprotIDQ8N3J5;V9GYZ5;A0A0A0MQZ4;V9GY69;V9GYI6;V9GYS8
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr4:88258441-88260375:-ENST00000608933.4ENSG00000163644.13PPM1KUTR3AluSx1,AluSx4,AluJo,AluScchr4:88258441-88260375:-.alignment
chr4:88261710-88262043:-ENST00000295908.10ENSG00000163644.13PPM1KUTR3(T)n,AluSq2chr4:88261710-88262043:-.alignment
chr4:88261710-88262043:-ENST00000608933.4ENSG00000163644.13PPM1KUTR3(T)n,AluSq2chr4:88261710-88262043:-.alignment


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2. Tumor-specific enriched editing regions for PPM1K


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
ENSG00000163644.13,PPM1KKIRCEAG1.2487e-15image
chr4:88258441-88260375:-KIRPEER1.1262e-07image
ENSG00000163644.13,PPM1KKIRPEAG1.4108e-07image
ENSG00000163644.13,PPM1KLUSCEAG3.4855e-03image
chr4:88258441-88260375:-UCECEER3.4952e-11image
ENSG00000163644.13,PPM1KUCECEAG5.8438e-10image


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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


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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
ENSG00000163644.13,PPM1KACCEAG3.3231e-023.2241e-022.4353e+07image
chr4:88258441-88260375:-ESCAEER3.2063e-024.1827e-025.0255e+03image
ENSG00000163644.13,PPM1KKIRPEAG1.0625e-023.1322e-021.4398e+06image

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3. Enriched editing regions and immune related genes for PPM1K


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

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4. Enriched editing regions and immune related splicing for PPM1K


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

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5. Enriched editing regions and immune infiltration for PPM1K


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
chr4:88258441-88260375:-ACCEERNK_cells_activated5.2655e-03-0.4679image
ENSG00000163644.13,PPM1KACCEAGNK_cells_activated4.1470e-03-0.4726image
ENSG00000163644.13,PPM1KBLCAEAGT_cells_follicular_helper1.8014e-020.2972image
chr4:88258441-88260375:-BRCAEERT_cells_CD4_memory_resting6.2440e-03-0.1323image
ENSG00000163644.13,PPM1KBRCAEAGMast_cells_resting9.5484e-03-0.1232image
chr4:88258441-88260375:-CESCEERB_cells_naive2.6061e-02-0.3316image
ENSG00000163644.13,PPM1KCESCEAGB_cells_naive2.3392e-02-0.3268image
chr4:88258441-88260375:-ESCAEERT_cells_gamma_delta1.1727e-030.4684image
ENSG00000163644.13,PPM1KESCAEAGB_cells_memory4.9600e-02-0.2409image
chr4:88258441-88260375:-GBMEERT_cells_CD4_memory_activated1.1990e-020.2133image
ENSG00000163644.13,PPM1KGBMEAGT_cells_CD4_memory_activated8.2600e-030.2232image
ENSG00000163644.13,PPM1KHNSCEAGB_cells_naive2.0961e-03-0.3184image
ENSG00000163644.13,PPM1KKIRCEAGT_cells_regulatory_(Tregs)1.5564e-020.2071image
chr4:88258441-88260375:-LGGEERT_cells_CD82.0475e-040.1665image
ENSG00000163644.13,PPM1KLGGEAGT_cells_CD81.5869e-040.1693image
chr4:88258441-88260375:-LIHCEERMacrophages_M01.2105e-020.3392image
ENSG00000163644.13,PPM1KLIHCEAGMacrophages_M04.3444e-020.2574image
ENSG00000163644.13,PPM1KLUSCEAGDendritic_cells_resting5.1080e-03-0.2689image
chr4:88258441-88260375:-OVEERB_cells_memory2.8280e-020.1978image
chr4:88261710-88262043:-OVEERT_cells_follicular_helper3.2286e-02-0.3064image
ENSG00000163644.13,PPM1KPAADEAGMast_cells_resting5.4241e-030.3914image
chr4:88258441-88260375:-PCPGEEREosinophils3.3646e-020.2242image
ENSG00000163644.13,PPM1KPCPGEAGEosinophils2.2314e-020.2380image
chr4:88258441-88260375:-PRADEERT_cells_regulatory_(Tregs)6.7712e-040.1902image
ENSG00000163644.13,PPM1KPRADEAGT_cells_regulatory_(Tregs)7.0068e-040.1888image
chr4:88258441-88260375:-SARCEERMast_cells_resting6.9959e-03-0.2593image
ENSG00000163644.13,PPM1KSARCEAGMast_cells_resting2.3215e-03-0.2888image
chr4:88258441-88260375:-STADEERT_cells_CD4_memory_activated1.2355e-020.2180image
ENSG00000163644.13,PPM1KSTADEAGMonocytes1.9216e-020.1832image
chr4:88258441-88260375:-TGCTEERT_cells_regulatory_(Tregs)5.9067e-03-0.3803image
ENSG00000163644.13,PPM1KTGCTEAGT_cells_regulatory_(Tregs)3.5652e-03-0.4008image
chr4:88258441-88260375:-THCAEERB_cells_naive1.6512e-02-0.1563image
ENSG00000163644.13,PPM1KTHCAEAGB_cells_naive1.0558e-02-0.1648image
ENSG00000163644.13,PPM1KTHYMEAGDendritic_cells_resting1.9910e-020.4454image


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6. Enriched editing regions and immune gene sets for PPM1K


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
ENSG00000163644.13,PPM1KLUSCEAG5.1861e-03image1.7067e-02-0.2302image


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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
chr4:88258441-88260375:-ACCGSVA_HALLMARK_APICAL_JUNCTIONEER1.8955e-020.4004image
ENSG00000163644.13,PPM1KACCGSVA_HALLMARK_FATTY_ACID_METABOLISMEAG2.1274e-02-0.3880image
ENSG00000163644.13,PPM1KBLCAGSVA_HALLMARK_ADIPOGENESISEAG3.4825e-020.2664image
chr4:88258441-88260375:-BRCAGSVA_HALLMARK_GLYCOLYSISEER2.0445e-040.1790image
ENSG00000163644.13,PPM1KBRCAGSVA_HALLMARK_GLYCOLYSISEAG8.8889e-040.1575image
chr4:88258441-88260375:-CESCGSVA_HALLMARK_PANCREAS_BETA_CELLSEER1.2803e-02-0.3683image
ENSG00000163644.13,PPM1KCESCGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG2.2802e-02-0.3281image
ENSG00000163644.13,PPM1KGBMGSVA_HALLMARK_MTORC1_SIGNALINGEAG1.6150e-030.2650image
chr4:88258441-88260375:-GBMGSVA_HALLMARK_MTORC1_SIGNALINGEER5.7530e-040.2894image
ENSG00000163644.13,PPM1KHNSCGSVA_HALLMARK_ALLOGRAFT_REJECTIONEAG2.1480e-02-0.2408image
ENSG00000163644.13,PPM1KKICHGSVA_HALLMARK_FATTY_ACID_METABOLISMEAG3.4631e-020.3746image
ENSG00000163644.13,PPM1KKIRCGSVA_HALLMARK_KRAS_SIGNALING_DNEAG2.7922e-030.2545image
chr4:88258441-88260375:-KIRPGSVA_HALLMARK_PROTEIN_SECRETIONEER2.4960e-02-0.2460image
ENSG00000163644.13,PPM1KLAMLGSVA_HALLMARK_P53_PATHWAYEAG2.3130e-020.4931image
chr4:88261710-88262043:-LGGGSVA_HALLMARK_PROTEIN_SECRETIONEER4.1559e-02-0.3948image
ENSG00000163644.13,PPM1KLGGGSVA_HALLMARK_MITOTIC_SPINDLEEAG3.0149e-04-0.1621image
chr4:88258441-88260375:-LGGGSVA_HALLMARK_MITOTIC_SPINDLEEER2.8946e-04-0.1626image
ENSG00000163644.13,PPM1KLIHCGSVA_HALLMARK_UV_RESPONSE_DNEAG8.4391e-03-0.3317image
chr4:88258441-88260375:-LIHCGSVA_HALLMARK_UV_RESPONSE_DNEER4.3644e-03-0.3820image
chr4:88258441-88260375:-LUADGSVA_HALLMARK_UNFOLDED_PROTEIN_RESPONSEEER5.3884e-030.2211image
ENSG00000163644.13,PPM1KLUADGSVA_HALLMARK_UNFOLDED_PROTEIN_RESPONSEEAG7.0315e-030.2085image
ENSG00000163644.13,PPM1KLUSCGSVA_HALLMARK_MYC_TARGETS_V2EAG4.8552e-050.3822image
chr4:88258441-88260375:-OVGSVA_HALLMARK_PANCREAS_BETA_CELLSEER5.8513e-040.3057image
ENSG00000163644.13,PPM1KOVGSVA_HALLMARK_PANCREAS_BETA_CELLSEAG2.2156e-030.2480image
ENSG00000163644.13,PPM1KPAADGSVA_HALLMARK_GLYCOLYSISEAG3.1228e-030.4138image
ENSG00000163644.13,PPM1KPRADGSVA_HALLMARK_HEME_METABOLISMEAG2.1489e-05-0.2355image
chr4:88258441-88260375:-PRADGSVA_HALLMARK_ANDROGEN_RESPONSEEER9.6492e-05-0.2176image
chr4:88258441-88260375:-SARCGSVA_HALLMARK_MYC_TARGETS_V2EER7.5453e-070.4569image
ENSG00000163644.13,PPM1KSARCGSVA_HALLMARK_MYC_TARGETS_V2EAG1.0957e-060.4471image
chr4:88258441-88260375:-SKCMGSVA_HALLMARK_PROTEIN_SECRETIONEER3.6699e-05-0.3075image
ENSG00000163644.13,PPM1KSKCMGSVA_HALLMARK_PROTEIN_SECRETIONEAG3.4223e-07-0.3681image
chr4:88261710-88262043:-STADGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEER1.6535e-02-0.2856image
chr4:88258441-88260375:-STADGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEER1.9527e-050.3637image
ENSG00000163644.13,PPM1KTGCTGSVA_HALLMARK_UNFOLDED_PROTEIN_RESPONSEEAG5.9455e-050.5317image
chr4:88258441-88260375:-TGCTGSVA_HALLMARK_MYC_TARGETS_V1EER1.3858e-040.5086image
chr4:88258441-88260375:-UCECGSVA_HALLMARK_XENOBIOTIC_METABOLISMEER4.0667e-020.3697image


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7. Enriched editing regions and drugs for PPM1K


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
chr4:88258441-88260375:-ACCBX.795EER6.5448e-03-0.4573image
ENSG00000163644.13,PPM1KACCKU.55933EAG6.2967e-03-0.4529image
ENSG00000163644.13,PPM1KBLCAFH535EAG2.2513e-03-0.3781image
chr4:88258441-88260375:-BRCAATRAEER6.5651e-050.1926image
ENSG00000163644.13,PPM1KBRCAAxitinibEAG8.1200e-04-0.1589image
ENSG00000163644.13,PPM1KCESCBryostatin.1EAG1.5020e-02-0.3491image
chr4:88258441-88260375:-CESCBryostatin.1EER5.6681e-03-0.4059image
chr4:88261710-88262043:-ESCAATRAEER3.0657e-03-0.4798image
ENSG00000163644.13,PPM1KGBMBIRB.0796EAG3.8473e-020.1758image
chr4:88258441-88260375:-GBMCCT007093EER2.3412e-030.2570image
ENSG00000163644.13,PPM1KHNSCIPA.3EAG3.8194e-040.3645image
ENSG00000163644.13,PPM1KKICHGemcitabineEAG1.8353e-020.4145image
ENSG00000163644.13,PPM1KKIRCBMS.536924EAG6.4210e-06-0.3761image
ENSG00000163644.13,PPM1KKIRPBMS.754807EAG9.9117e-03-0.2662image
chr4:88258441-88260375:-KIRPAZD6244EER7.1973e-04-0.3639image
ENSG00000163644.13,PPM1KLGGAZD6482EAG5.6615e-080.2415image
chr4:88258441-88260375:-LGGAZD6482EER7.2468e-080.2396image
ENSG00000163644.13,PPM1KLIHCAICAREAG8.4062e-080.6186image
chr4:88258441-88260375:-LIHCAZD6482EER8.9333e-070.6117image
ENSG00000163644.13,PPM1KLUADAZD6244EAG7.5248e-030.2068image
chr4:88258441-88260375:-LUADAZD6244EER3.3917e-030.2325image
ENSG00000163644.13,PPM1KLUSCEpothilone.BEAG4.8577e-04-0.3316image
chr4:88261710-88262043:-OVAG.014699EER1.6809e-030.4372image
chr4:88258441-88260375:-OVAZD6482EER1.1275e-030.2903image
ENSG00000163644.13,PPM1KOVLFM.A13EAG5.6099e-030.2251image
ENSG00000163644.13,PPM1KPAADFTI.277EAG2.6108e-03-0.4207image
ENSG00000163644.13,PPM1KPCPGBIRB.0796EAG2.2639e-030.3145image
chr4:88258441-88260375:-PCPGBIRB.0796EER1.2070e-030.3360image
chr4:88258441-88260375:-PRADGNF.2EER2.4450e-09-0.3280image
ENSG00000163644.13,PPM1KPRADGNF.2EAG3.0913e-09-0.3246image
ENSG00000163644.13,PPM1KSARCLapatinibEAG1.0239e-040.3635image
chr4:88258441-88260375:-SARCCCT007093EER2.6855e-040.3454image
ENSG00000163644.13,PPM1KSKCMBMS.509744EAG1.0715e-05-0.3208image
chr4:88258441-88260375:-SKCMBMS.509744EER6.8217e-05-0.2972image
ENSG00000163644.13,PPM1KSTADAxitinibEAG4.4042e-030.2220image
chr4:88258441-88260375:-STADGDC0941EER5.1086e-050.3462image
chr4:88261710-88262043:-STADCCT018159EER6.0770e-040.3997image
ENSG00000163644.13,PPM1KTGCTAKT.inhibitor.VIIIEAG5.4788e-040.4672image
chr4:88258441-88260375:-TGCTAKT.inhibitor.VIIIEER3.4843e-040.4814image
chr4:88258441-88260375:-THCAElesclomolEER3.7215e-02-0.1360image
ENSG00000163644.13,PPM1KTHCABexaroteneEAG4.0441e-020.1324image


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