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Center for Computational Systems Medicine
Soverview

Gene summary

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RNA A-to-I events

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Differntial gene expression between RNA A-to-I edited versus non-edited samples

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Protein coding region RNA A-to-I editings

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The effects of the RNA editing to the miRNA binding sites

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The effects of the RNA editing to the stability of the RNA structures

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Relation with ADAR

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Relation with AD stages

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Related drugs with this gene

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Related diseases with this gene


Gene summary for PEX2

check button Gene summary
Gene informationGene symbol

PEX2

Gene ID

5828

Gene nameperoxisomal biogenesis factor 2
SynonymsPAF1|PBD5A|PBD5B|PMP3|PMP35|PXMP3|RNF72|ZWS3
Cytomap

8q21.13

Type of geneprotein-coding
Descriptionperoxisome biogenesis factor 235 kDa peroxisomal membrane proteinRING finger protein 72peroxisomal membrane protein 3, 35kDaperoxisome assembly factor 1
Modification date20200313
UniProtAcc

P28328,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID

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RNA A-to-I events for PEX2

check buttonRNA A-to-I editing events in the ROSMAP, MSBB, and Mayo data sets based on Ensembl gene isoform structure.
* This pie chart shows the number of RNA A-to-I editing events in different types of transcripts (# event, percentage).
all structure

check button RNA editing frequencies across three data sets.
boxplot

check buttonThe number of RNA A-to-I editing events in different types of transcripts (# event, percentage).
boxplot

check button RNA A-to-I editing events in AD.
ADediting_1421877(76981214, -), ADediting_1421878(76982567, -), ADediting_1421879(76982568, -), ADediting_1421880(76982577, -), ADediting_1421881(76982618, -), ADediting_1421882(76982622, -), ADediting_1421883(76982643, -), ADediting_1421884(76982646, -), ADediting_1421885(76982697, -), ADediting_1421886(76982722, -), ADediting_1421887(76982723, -), ADediting_1421888(76982726, -), ADediting_1421889(76982746, -), ADediting_1591497(76981589, -), ADediting_1591498(76982555, -),

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RNA editing positional annotations for PEX2 using Annovar

check button Protein coding RNA editing(s).
ADeditome IDPositionVariant typeENSTNTchangeAAchangeSIFT_scorePolyphen2_HVAR_scorePROVEAN_pred

check button Gene structure information of RNA editing(s).
ADeditome IDPositionVariant type
ADediting_1421877chr8_76981214_-UTR3
ADediting_1421878chr8_76982567_-UTR3
ADediting_1421879chr8_76982568_-UTR3
ADediting_1421880chr8_76982577_-UTR3
ADediting_1421881chr8_76982618_-UTR3
ADediting_1421882chr8_76982622_-UTR3
ADediting_1421883chr8_76982643_-UTR3
ADediting_1421884chr8_76982646_-UTR3
ADediting_1421885chr8_76982697_-UTR3
ADediting_1421886chr8_76982722_-UTR3
ADediting_1421887chr8_76982723_-UTR3
ADediting_1421888chr8_76982726_-UTR3
ADediting_1421889chr8_76982746_-UTR3
ADediting_1591497chr8_76981589_-UTR3
ADediting_1591498chr8_76982555_-UTR3

check button Repat-regional RNA editing(s).
ADeditome IDPositionRepeat familyRepeat sub familyRepeat name
ADediting_1421877chr8_76981214_-SINEAluName=AluJb
ADediting_1421878chr8_76982567_-SINEAluName=AluSc8
ADediting_1421879chr8_76982568_-SINEAluName=AluSc8
ADediting_1421880chr8_76982577_-SINEAluName=AluSc8
ADediting_1421881chr8_76982618_-SINEAluName=AluSc8
ADediting_1421882chr8_76982622_-SINEAluName=AluSc8
ADediting_1421883chr8_76982643_-SINEAluName=AluSc8
ADediting_1421884chr8_76982646_-SINEAluName=AluSc8
ADediting_1421885chr8_76982697_-SINEAluName=AluSc8
ADediting_1421886chr8_76982722_-SINEAluName=AluSc8
ADediting_1421887chr8_76982723_-SINEAluName=AluSc8
ADediting_1421888chr8_76982726_-SINEAluName=AluSc8
ADediting_1421889chr8_76982746_-SINEAluName=AluSc8
ADediting_1591497chr8_76981589_-SINEAluName=AluJo
ADediting_1591498chr8_76982555_-SINEAluName=AluSc8

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RNA A-to-I editing events in the alternative splicing sites for PEX2

check button RNA A-to-I editing(s) in the alternative splicing sites.
AStypeADeditomIDEditing positionAS positionAS directionExonic locationWildtype sequenceWildtype splicing strengthRNA edited sequenceRNA edited splicing strength

check button Differential pencent of spliced in (PSI) between RNA A-to-I edited and non-edited samples

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for PEX2

check button Distribution of the averaged gene expression in AD and control with or without RNA A-to-I editing event.
* The grey color means N/A.
boxplot

check button Distribution of the averaged gene isoform expression in AD and control with or without RNA A-to-I editing event.
boxplot
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check button - Differentially expressed gene between RNA A-to-I edited samples versus non-edited samples.
* Click on the image to enlarge it in a new window.
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check button - Differentially expressed transcript between RNA A-to-I edited samples versus non-edited samples.
* Click on the image to enlarge it in a new window.

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ADeditome IDChrPositoingSkipped exonENSGENSTs

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Protein coding region RNA A-to-I editings for PEX2

check button- Lollipop plot for RNA A-to-I editings across protein structure.
* Click on the image to enlarge it in a new window.


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The effects of the RNA editing to the miRNA binding sites for PEX2

check buttonRNA A-to-I editings in the ROSMAP, MSBB, and Mayo data sets based on Ensembl gene isoform structure.
all structure

check button RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
ADediting_1421878chr8_76982567_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-3189-3pchr876982566769825727mer-m87698256576982588157-27.21
ADediting_1421878chr8_76982567_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-6813-3pchr876982565769825717mer-m87698256476982584140-12.88
ADediting_1421879chr8_76982568_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-326chr876982566769825727mer-m87698256576982584140-14.45
ADediting_1421879chr8_76982568_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-330-5pchr876982566769825727mer-m87698256576982586148-23.39
ADediting_1421879chr8_76982568_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-4314chr876982567769825737mer-m87698256676982583140-19.43
ADediting_1421879chr8_76982568_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-514a-5pchr876982565769825717mer-m87698256476982587155-21.45
ADediting_1421880chr8_76982577_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-6089chr876982572769825787mer-m87698257176982593156-34.32
ADediting_1421882chr8_76982622_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-3190-5pchr876982617769826237mer-m87698261676982634148-20.6
ADediting_1421882chr8_76982622_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-548schr876982618769826247mer-m87698261776982639149-16.48
ADediting_1421885chr8_76982697_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-4691-3pchr876982693769826997mer-m87698269276982719150-26.36
ADediting_1421886chr8_76982722_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-146a-5pchr876982717769827237mer-m87698271676982738147-21.66
ADediting_1421886chr8_76982722_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-146b-5pchr876982717769827237mer-m87698271676982742152-20.63
ADediting_1421886chr8_76982722_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-7153-5pchr876982717769827237mer-m87698271676982739148-22.32
ADediting_1421889chr8_76982746_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-17-3pchr876982746769827527mer-m87698274576982767153-18.76
ADediting_1591497chr8_76981589_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-4252chr876981585769815917mer-m87698158476981603160-25.3
ADediting_1591497chr8_76981589_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-5008-3pchr876981589769815957mer-m87698158876981605146-17.64
ADediting_1591497chr8_76981589_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-7157-3pchr876981589769815957mer-m87698158876981608146-14.66

check button RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
ADediting_1421879chr8_76982568_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-887-5pchr876982567769825748mer-1a7698256776982586143-15.14
ADediting_1421880chr8_76982577_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-4478chr876982573769825797mer-m87698257276982587145-20.53
ADediting_1421881chr8_76982618_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-4794chr876982617769826237mer-m87698261676982637152-19.2
ADediting_1421881chr8_76982618_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-664a-5pchr876982617769826237mer-m87698261676982638148-14.15
ADediting_1421882chr8_76982622_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-4794chr876982617769826237mer-m87698261676982637152-19.2
ADediting_1421882chr8_76982622_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-664a-5pchr876982617769826237mer-m87698261676982638148-14.15
ADediting_1421883chr8_76982643_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-3675-3pchr876982638769826447mer-m87698263776982658145-12.58
ADediting_1421885chr8_76982697_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-5690chr876982693769826997mer-m87698269276982712145-16.75
ADediting_1421886chr8_76982722_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-219b-3pchr876982719769827257mer-m87698271876982738153-15.53
ADediting_1421886chr8_76982722_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-302fchr876982720769827267mer-m87698271976982735145-8.09
ADediting_1421887chr8_76982723_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-219b-3pchr876982719769827257mer-m87698271876982738153-15.53
ADediting_1421887chr8_76982723_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-302fchr876982720769827267mer-m87698271976982735145-8.09
ADediting_1421889chr8_76982746_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-6516-5pchr876982746769827527mer-m87698274576982767152-16.77
ADediting_1591497chr8_76981589_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-4289chr876981587769815937mer-m87698158676981604153-15.56
ADediting_1591498chr8_76982555_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-3686chr876982551769825577mer-m87698255076982571140-11.18

check button RNA A-to-I editing in lncRNA gained miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in lncRNA lost miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs gained binding to lncRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs lost binding to lncRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
ADediting_1337757chr7_5495852_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-589-3pchr876982790769827967mer-m87698278976982813158-22.45
ADediting_843620chr2_207754818_+ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-4775chr876981750769817578mer-1a7698175076981771158-11.06
ADediting_843620chr2_207754818_+ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-4775chr876981952769819598mer-1a7698195276981975153-10.42

check button RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
ADediting_1337758chr7_5495892_-ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-589-5pchr876980994769810007mer-m87698099376981012152-20.32
ADediting_843620chr2_207754818_+ENSG00000164751.15ENST00000357039.9PEX2-201hsa-miR-4775chr876981662769816687mer-m87698166176981682145-2

check button Differentially expressed gene-miRNA network
Differentially expressed mRNA-miRNA network
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The effects of the RNA editing to the stability of the RNA structures for PEX2

check button - RNA A-to-I editing in mRNA.
* Click on the image to enlarge it in a new window.
ENSTENST typeRNA structure without RNA A-to-I editing.RNA structure with RNA A-to-I editing.
ENST00000357039.9protein_codingSoverviewSoverview

check button RNA A-to-I editing in miRNA.
ADeditom_IDENSTmir_IDEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

check button RNA A-to-I editing in mRNA.
ADeditom_IDENSTEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI
ADediting_1421877ENST00000357039.9chr8_76981214_-3213-1184.40-1182.80-1205.60
ADediting_1591497ENST00000357039.9chr8_76981589_-2838-1188.40-1182.80-1205.60
ADediting_1591498ENST00000357039.9chr8_76982555_-1872-1184.30-1182.80-1205.60
ADediting_1421878ENST00000357039.9chr8_76982567_-1860-1184.30-1182.80-1205.60
ADediting_1421879ENST00000357039.9chr8_76982568_-1859-1184.40-1182.80-1205.60
ADediting_1421880ENST00000357039.9chr8_76982577_-1850-1182.10-1182.80-1205.60
ADediting_1421881ENST00000357039.9chr8_76982618_-1809-1183.60-1182.80-1205.60
ADediting_1421882ENST00000357039.9chr8_76982622_-1805-1187.30-1182.80-1205.60
ADediting_1421883ENST00000357039.9chr8_76982643_-1784-1184.00-1182.80-1205.60
ADediting_1421884ENST00000357039.9chr8_76982646_-1781-1184.60-1182.80-1205.60
ADediting_1421885ENST00000357039.9chr8_76982697_-1730-1186.00-1182.80-1205.60
ADediting_1421886ENST00000357039.9chr8_76982722_-1705-1186.30-1182.80-1205.60
ADediting_1421887ENST00000357039.9chr8_76982723_-1704-1182.80-1182.80-1205.60
ADediting_1421888ENST00000357039.9chr8_76982726_-1701-1185.80-1182.80-1205.60
ADediting_1421889ENST00000357039.9chr8_76982746_-1681-1183.60-1182.80-1205.60

check button RNA A-to-I editing in lncRNA.
ADeditom_IDENSTEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

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Relation with ADAR for PEX2

check button Correlation between ADAR gene expression and RNA editing frequency
TissueADeditomIDpositionADAR1 (p-val)ADAR1 (coeff.)ADAR2 (p-val)ADAR2 (coeff.)ADAR3 (p-val)ADAR3 (coeff.)
CERADediting_1421880chr8_76982577_-0.0006787297227701370.2743983268640069.74020253480564e-050.312781916349470.01942294087633160.190681445129825
CERADediting_1421881chr8_76982618_-0.006789402718188510.220148935594057.21979128831025e-080.4224999470576030.1570133877373850.116129754722608
CERADediting_1421882chr8_76982622_-0.002821475402353530.2422345349194981.05084617867738e-060.3862540401465960.108539662612350.131561073218434
CERADediting_1421889chr8_76982746_-0.02242163293591880.1863412410356996.7565869065172e-050.3194547186507460.002095476080799530.249290904760674

check button Correlation between ADAR gene expression and this gene's expression
TissueADAR1 (p-val)ADAR1 (coeff.)ADAR2 (p-val)ADAR2 (coeff.)ADAR3 (p-val)ADAR3 (coeff.)
DLPFC4.39120779341651e-210.5007886304743351.16155150927752e-090.3368394340317324.2067064942696e-050.230420158698647
AC6.63886396337806e-480.7578788077440953.89336213102065e-260.6029262692312341.38909023007753e-240.587401116474914
PCC2.29625663478248e-100.438216338574351.13537174694983e-080.398478098618850.0001592359377492540.269919345146743
CER6.24474151013374e-250.716659669513645.14269006602057e-090.4545128656525374.24566860914583e-090.456711906316712
TCX1.06779308870428e-110.5185454917175810.7575977047881020.025408587196712.92332284754936e-130.550498562481451
FP1.47250277905343e-120.498255226546043.61540102474294e-130.509876255147820.006427641210683770.203548239813114
PG2.79568905875786e-510.8423417826355612.19879408975179e-170.5695308096431350.3297841320733670.0718493401207214
STG1.82563243611044e-150.7345834268499123.82833081486635e-090.5888453517350.01978677753792320.253886681449282

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Relation with AD stages for PEX2

check button Correlation between AD stages and RNA editing frequency
TissueADeditomIDpositionP-valCoeff.
CERADediting_1421882chr8_76982622_-8.15064847129555e-050.369886537590384
IFGADediting_1421882chr8_76982622_-0.006790780353380570.527024363859863

check button Correlation between AD stages and this gene's expression
TissueP-valCoeff.
CER0.0001334582277725810.359399986360764
TCX1.99256511383149e-080.512228853335936
IFG0.0242891808127566-0.449185595620075

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RelatedDrugs for PEX2

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for PEX2

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
PEX2C1832200Peroxisome biogenesis disorders2CTD_human
PEX2C0043459Zellweger Syndrome1CTD_human;ORPHANET
PEX2C0282527Infantile Refsum Disease (disorder)1CTD_human;ORPHANET
PEX2C0751594Zellweger-Like Syndrome1CTD_human
PEX2C3542026PEROXISOME BIOGENESIS DISORDER 5B1CTD_human;UNIPROT
PEX2C3658299Zellweger Spectrum1CTD_human