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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: HMGB1 (ImmuneEditome ID:3146)

1. Gene summary of enriched editing regions for HMGB1

check button Gene summary
Gene informationGene symbol

HMGB1

Gene ID

3146

GeneSynonymsHMG-1|HMG1|HMG3|SBP-1
GeneCytomap

13q12.3

GeneTypeprotein-coding
GeneDescriptionhigh mobility group protein B1|Amphoterin|Sulfoglucuronyl carbohydrate binding protein|high-mobility group (nonhistone chromosomal) protein 1
GeneModificationdate20230530
UniprotIDQ5T7C4;P09429;A0A024RDR0
PubMed ID

check buttonUCSC image.
all structure

check buttonLocations of each EERs.
EERENSTENSGGeneNameRegionRepeatdsRNA structure
chr13:30457212-30457549:-ENST00000341423.8ENSG00000189403.13HMGB1UTR3AluJr,FLAM_Cchr13:30457212-30457549:-.alignment
chr13:30586160-30586709:-ENST00000405805.4ENSG00000189403.13HMGB1intronicAluSx,AluJb,L2chr13:30586160-30586709:-.alignment
chr13:30597172-30597499:-ENST00000405805.4ENSG00000189403.13HMGB1intronicMLT1Cchr13:30597172-30597499:-.alignment


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2. Tumor-specific enriched editing regions for HMGB1


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
chr13:30457212-30457549:-BRCAEER9.6984e-10image
ENSG00000189403.13,HMGB1BRCAEAG9.5470e-11image
chr13:30457212-30457549:-LUSCEER3.8667e-02image
ENSG00000189403.13,HMGB1LUSCEAG3.8316e-02image
chr13:30457212-30457549:-THCAEER1.1119e-03image
ENSG00000189403.13,HMGB1THCAEAG1.0683e-03image


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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
ENSG00000189403.13,HMGB1THCAPathEAG6.4368e-054.8640e-040.1939image
chr13:30457212-30457549:-THCAPathEER1.6232e-041.0020e-030.1836image


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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 HMGB1


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 HMGB1


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 HMGB1


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
ENSG00000189403.13,HMGB1BLCAEAGMacrophages_M13.3812e-030.2809image
chr13:30457212-30457549:-BRCAEERB_cells_naive8.3090e-06-0.1624image
ENSG00000189403.13,HMGB1BRCAEAGB_cells_naive1.2685e-06-0.1755image
chr13:30457212-30457549:-CESCEERB_cells_naive2.8730e-03-0.2645image
ENSG00000189403.13,HMGB1CESCEAGB_cells_naive3.0985e-03-0.2625image
ENSG00000189403.13,HMGB1COADEAGMast_cells_activated1.2427e-030.3708image
chr13:30457212-30457549:-ESCAEERMacrophages_M12.8120e-020.2290image
ENSG00000189403.13,HMGB1ESCAEAGMacrophages_M12.9067e-020.2264image
chr13:30457212-30457549:-GBMEERMonocytes1.6898e-020.2264image
ENSG00000189403.13,HMGB1GBMEAGMonocytes1.6898e-020.2264image
chr13:30457212-30457549:-KIRCEEREosinophils1.1826e-020.1452image
ENSG00000189403.13,HMGB1KIRCEAGDendritic_cells_activated6.7224e-030.1554image
ENSG00000189403.13,HMGB1KIRPEAGT_cells_CD4_memory_resting1.7442e-03-0.3187image
chr13:30457212-30457549:-LGGEEREosinophils1.7538e-020.1150image
ENSG00000189403.13,HMGB1LGGEAGEosinophils1.7423e-020.1152image
chr13:30457212-30457549:-LIHCEERMast_cells_activated9.7562e-030.2250image
ENSG00000189403.13,HMGB1LIHCEAGMast_cells_activated9.7562e-030.2250image
chr13:30457212-30457549:-LUADEERT_cells_CD4_memory_activated3.8224e-030.2296image
ENSG00000189403.13,HMGB1LUADEAGT_cells_CD4_memory_activated1.5122e-030.2473image
chr13:30457212-30457549:-LUSCEERMacrophages_M01.6116e-02-0.1782image
ENSG00000189403.13,HMGB1LUSCEAGMacrophages_M01.5922e-02-0.1780image
ENSG00000189403.13,HMGB1MESOEAGT_cells_CD86.5212e-030.4856image
chr13:30457212-30457549:-OVEERT_cells_follicular_helper5.8632e-030.1937image
ENSG00000189403.13,HMGB1OVEAGT_cells_follicular_helper7.0204e-030.1882image
chr13:30457212-30457549:-PAADEERDendritic_cells_activated9.2786e-030.2910image
ENSG00000189403.13,HMGB1PAADEAGDendritic_cells_activated9.2786e-030.2910image
ENSG00000189403.13,HMGB1PCPGEAGMast_cells_resting4.0269e-03-0.3785image
ENSG00000189403.13,HMGB1PRADEAGPlasma_cells7.1804e-03-0.2151image
chr13:30457212-30457549:-SARCEERDendritic_cells_activated2.1568e-020.2273image
ENSG00000189403.13,HMGB1SARCEAGDendritic_cells_activated2.1568e-020.2273image
chr13:30457212-30457549:-SKCMEERT_cells_CD4_memory_resting7.1472e-03-0.2280image
ENSG00000189403.13,HMGB1SKCMEAGT_cells_CD4_memory_resting7.1755e-03-0.2279image
chr13:30457212-30457549:-STADEERT_cells_CD81.9400e-030.2258image
ENSG00000189403.13,HMGB1STADEAGMacrophages_M01.5389e-03-0.2198image
chr13:30457212-30457549:-THCAEERT_cells_regulatory_(Tregs)3.5176e-050.2287image
ENSG00000189403.13,HMGB1THCAEAGT_cells_regulatory_(Tregs)3.1128e-050.2295image
ENSG00000189403.13,HMGB1THYMEAGMacrophages_M07.0412e-040.5194image
ENSG00000189403.13,HMGB1UCSEAGMacrophages_M21.4803e-030.6618image


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6. Enriched editing regions and immune gene sets for HMGB1


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
ENSG00000189403.13,HMGB1BLCAGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEAG1.1801e-030.3095image
ENSG00000189403.13,HMGB1BRCAGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG4.6694e-110.2368image
chr13:30457212-30457549:-BRCAGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER1.9054e-160.2950image
ENSG00000189403.13,HMGB1CESCGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG2.6080e-040.3211image
chr13:30457212-30457549:-CESCGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER1.1883e-040.3375image
ENSG00000189403.13,HMGB1CHOLGSVA_HALLMARK_PEROXISOMEEAG1.2569e-02-0.5344image
ENSG00000189403.13,HMGB1COADGSVA_HALLMARK_DNA_REPAIREAG4.1099e-04-0.4028image
chr13:30457212-30457549:-ESCAGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEER6.1414e-040.3505image
ENSG00000189403.13,HMGB1ESCAGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG1.0582e-030.3343image
ENSG00000189403.13,HMGB1GBMGSVA_HALLMARK_BILE_ACID_METABOLISMEAG1.1864e-040.3572image
chr13:30457212-30457549:-GBMGSVA_HALLMARK_BILE_ACID_METABOLISMEER1.1864e-040.3572image
ENSG00000189403.13,HMGB1HNSCGSVA_HALLMARK_MYC_TARGETS_V2EAG3.9268e-020.2045image
chr13:30457212-30457549:-KIRCGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER1.5327e-03-0.1822image
ENSG00000189403.13,HMGB1KIRCGSVA_HALLMARK_NOTCH_SIGNALINGEAG5.9704e-05-0.2285image
ENSG00000189403.13,HMGB1KIRPGSVA_HALLMARK_TGF_BETA_SIGNALINGEAG6.1448e-03-0.2807image
chr13:30457212-30457549:-LGGGSVA_HALLMARK_MITOTIC_SPINDLEEER5.8410e-06-0.2176image
ENSG00000189403.13,HMGB1LGGGSVA_HALLMARK_MITOTIC_SPINDLEEAG5.1874e-06-0.2188image
chr13:30457212-30457549:-LIHCGSVA_HALLMARK_PEROXISOMEEER4.2829e-030.2480image
ENSG00000189403.13,HMGB1LIHCGSVA_HALLMARK_PEROXISOMEEAG4.2829e-030.2480image
chr13:30457212-30457549:-LUADGSVA_HALLMARK_ALLOGRAFT_REJECTIONEER6.5709e-030.2161image
ENSG00000189403.13,HMGB1LUADGSVA_HALLMARK_PEROXISOMEEAG3.6245e-03-0.2273image
chr13:30457212-30457549:-LUSCGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER3.0763e-050.3037image
ENSG00000189403.13,HMGB1LUSCGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG2.6894e-050.3050image
ENSG00000189403.13,HMGB1MESOGSVA_HALLMARK_CHOLESTEROL_HOMEOSTASISEAG3.9027e-020.3787image
ENSG00000189403.13,HMGB1OVGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG4.3232e-050.2822image
chr13:30457212-30457549:-OVGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER1.6124e-050.2991image
chr13:30457212-30457549:-PAADGSVA_HALLMARK_GLYCOLYSISEER1.2125e-020.2810image
ENSG00000189403.13,HMGB1PAADGSVA_HALLMARK_GLYCOLYSISEAG1.2125e-020.2810image
ENSG00000189403.13,HMGB1PCPGGSVA_HALLMARK_MYC_TARGETS_V1EAG1.2621e-02-0.3313image
ENSG00000189403.13,HMGB1READGSVA_HALLMARK_P53_PATHWAYEAG4.6877e-02-0.3597image
chr13:30457212-30457549:-SARCGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEER5.4486e-03-0.2733image
ENSG00000189403.13,HMGB1SARCGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG5.4486e-03-0.2733image
chr13:30457212-30457549:-SKCMGSVA_HALLMARK_UV_RESPONSE_UPEER3.7867e-040.2984image
ENSG00000189403.13,HMGB1SKCMGSVA_HALLMARK_UV_RESPONSE_UPEAG3.8187e-040.2982image
ENSG00000189403.13,HMGB1STADGSVA_HALLMARK_MITOTIC_SPINDLEEAG1.0570e-05-0.3023image
chr13:30457212-30457549:-STADGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEER5.5796e-030.2025image
ENSG00000189403.13,HMGB1THCAGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEAG2.2863e-090.3247image
chr13:30457212-30457549:-THCAGSVA_HALLMARK_INTERFERON_GAMMA_RESPONSEEER1.7689e-090.3278image
ENSG00000189403.13,HMGB1THYMGSVA_HALLMARK_WNT_BETA_CATENIN_SIGNALINGEAG5.5592e-03-0.4357image
ENSG00000189403.13,HMGB1UCECGSVA_HALLMARK_NOTCH_SIGNALINGEAG1.9895e-06-0.5301image
chr13:30457212-30457549:-UCECGSVA_HALLMARK_NOTCH_SIGNALINGEER2.5171e-05-0.4905image
ENSG00000189403.13,HMGB1UCSGSVA_HALLMARK_INTERFERON_ALPHA_RESPONSEEAG8.9751e-030.5681image


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7. Enriched editing regions and drugs for HMGB1


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
ENSG00000189403.13,HMGB1BLCAEHT.1864EAG4.0595e-030.2756image
ENSG00000189403.13,HMGB1BRCAJNK.Inhibitor.VIIIEAG1.8779e-06-0.1728image
chr13:30457212-30457549:-BRCAAxitinibEER2.3088e-060.1721image
chr13:30457212-30457549:-CESCCI.1040EER2.1581e-05-0.3701image
ENSG00000189403.13,HMGB1CESCCI.1040EAG1.9268e-05-0.3721image
ENSG00000189403.13,HMGB1CHOLEmbelinEAG3.3359e-03-0.6098image
ENSG00000189403.13,HMGB1COADCCT007093EAG7.6137e-06-0.4973image
chr13:30457212-30457549:-ESCAJNK.Inhibitor.VIIIEER4.5726e-03-0.2931image
ENSG00000189403.13,HMGB1ESCAJNK.Inhibitor.VIIIEAG4.7902e-03-0.2901image
ENSG00000189403.13,HMGB1GBMCytarabineEAG3.2984e-040.3347image
chr13:30457212-30457549:-GBMCytarabineEER3.2984e-040.3347image
ENSG00000189403.13,HMGB1HNSCJNK.Inhibitor.VIIIEAG1.0040e-03-0.3210image
ENSG00000189403.13,HMGB1KIRCGW843682XEAG3.1338e-060.2641image
chr13:30457212-30457549:-KIRCEmbelinEER1.3008e-020.1432image
ENSG00000189403.13,HMGB1KIRPAZD8055EAG3.3370e-03-0.2997image
chr13:30457212-30457549:-LGGEmbelinEER3.5230e-080.2632image
ENSG00000189403.13,HMGB1LGGEmbelinEAG3.2512e-080.2638image
chr13:30457212-30457549:-LIHCGSK.650394EER1.4588e-020.2130image
ENSG00000189403.13,HMGB1LIHCGSK.650394EAG1.4588e-020.2130image
chr13:30457212-30457549:-LUADAG.014699EER1.0881e-02-0.2027image
ENSG00000189403.13,HMGB1LUADAG.014699EAG4.4276e-04-0.2729image
ENSG00000189403.13,HMGB1LUSCAZD6244EAG6.2337e-04-0.2506image
chr13:30457212-30457549:-LUSCAZD6244EER6.7640e-04-0.2497image
ENSG00000189403.13,HMGB1MESOABT.263EAG9.8893e-040.5708image
ENSG00000189403.13,HMGB1OVGW843682XEAG2.8472e-02-0.1534image
chr13:30457212-30457549:-OVBortezomibEER2.8246e-02-0.1548image
chr13:30457212-30457549:-PAADIPA.3EER4.9831e-030.3189image
ENSG00000189403.13,HMGB1PAADIPA.3EAG4.9831e-030.3189image
ENSG00000189403.13,HMGB1PCPGBI.D1870EAG6.0437e-040.4442image
ENSG00000189403.13,HMGB1PRADGW.441756EAG3.5776e-040.2831image
ENSG00000189403.13,HMGB1READBortezomibEAG2.0575e-02-0.4141image
chr13:30457212-30457549:-SARCGDC0941EER6.7136e-040.3313image
ENSG00000189403.13,HMGB1SARCGDC0941EAG6.7136e-040.3313image
chr13:30457212-30457549:-SKCMAG.014699EER2.0292e-030.2605image
ENSG00000189403.13,HMGB1SKCMAG.014699EAG1.8535e-030.2627image
chr13:30457212-30457549:-STADKU.55933EER9.4861e-04-0.2404image
ENSG00000189403.13,HMGB1STADJNJ.26854165EAG3.8286e-05-0.2834image
ENSG00000189403.13,HMGB1THCAAZD6244EAG3.7059e-10-0.3400image
chr13:30457212-30457549:-THCAAZD6244EER5.6015e-10-0.3377image
ENSG00000189403.13,HMGB1THYMAUY922EAG1.3899e-050.6354image
ENSG00000189403.13,HMGB1UCECAS601245EAG1.7053e-040.4317image
chr13:30457212-30457549:-UCECAS601245EER1.2010e-030.3874image
ENSG00000189403.13,HMGB1UCSCCT018159EAG6.2880e-030.5890image


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check button EAGs targeted by drugs from DrugBank database.
* EAG: EER-associated genes.
EERENSTUniprotIDDrugBankIDDrugDrugType
chr13:30457212-30457549:-ENST00000341423.8P09429DB00608ChloroquineSmallMoleculeDrug
chr13:30586160-30586709:-ENST00000405805.4P09429DB00608ChloroquineSmallMoleculeDrug
chr13:30597172-30597499:-ENST00000405805.4P09429DB00608ChloroquineSmallMoleculeDrug