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Center for Computational Systems Medicine
Soverview

Gene summary

Soverview

RNA A-to-I events

Soverview

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

Soverview

Protein coding region RNA A-to-I editings

Soverview

The effects of the RNA editing to the miRNA binding sites

Soverview

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

Soverview

Relation with ADAR

Soverview

Relation with AD stages

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Related drugs with this gene

Soverview

Related diseases with this gene


Gene summary for KDM1B

check button Gene summary
Gene informationGene symbol

KDM1B

Gene ID

221656

Gene namelysine demethylase 1B
SynonymsAOF1|C6orf193|LSD2
Cytomap

6p22.3

Type of geneprotein-coding
Descriptionlysine-specific histone demethylase 1Bflavin-containing amine oxidase domain-containing protein 1lysine (K)-specific demethylase 1Blysine-specific histone demethylase 2
Modification date20200313
UniProtAcc

Q8NB78,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
KDM1B

GO:0034720

histone H3-K4 demethylation

23266887


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RNA A-to-I events for KDM1B

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_1251296(18156715, +), ADediting_1251297(18156730, +), ADediting_1251298(18156731, +), ADediting_1251299(18159026, +), ADediting_1251300(18166590, +), ADediting_1251301(18166595, +), ADediting_1251302(18166756, +), ADediting_1251303(18166774, +), ADediting_1251304(18166779, +), ADediting_1251305(18166809, +), ADediting_1251306(18166817, +), ADediting_1251307(18167286, +), ADediting_1251308(18173866, +), ADediting_1251309(18173886, +), ADediting_1251310(18173911, +), ADediting_1251311(18183368, +), ADediting_1251312(18188877, +), ADediting_1251313(18188901, +), ADediting_1251314(18188913, +), ADediting_1251315(18188984, +), ADediting_1251316(18189019, +), ADediting_1251317(18189036, +), ADediting_1251318(18192951, +), ADediting_1251319(18193400, +), ADediting_1251320(18193406, +), ADediting_1251321(18193419, +), ADediting_1251322(18193436, +), ADediting_1251323(18193522, +), ADediting_1251324(18197981, +), ADediting_1251325(18197984, +), ADediting_1251326(18197995, +), ADediting_1251327(18198426, +), ADediting_1251328(18198438, +), ADediting_1251329(18198451, +), ADediting_1251330(18198598, +), ADediting_1251331(18198913, +), ADediting_1251332(18198973, +), ADediting_1251333(18198982, +), ADediting_1251334(18198983, +), ADediting_1251335(18198990, +), ADediting_1251336(18199051, +), ADediting_1251337(18199091, +), ADediting_1251338(18199092, +), ADediting_1251339(18199130, +), ADediting_1251340(18199158, +), ADediting_1251341(18199903, +), ADediting_1251342(18199934, +), ADediting_1251343(18200008, +), ADediting_1251344(18200071, +), ADediting_1251345(18200092, +), ADediting_1251346(18200095, +), ADediting_1251347(18210461, +), ADediting_1251348(18210470, +), ADediting_1251349(18210596, +), ADediting_1251350(18210600, +), ADediting_1251351(18210621, +), ADediting_1251352(18210623, +), ADediting_1251353(18210624, +), ADediting_1251354(18210743, +), ADediting_1251355(18210774, +), ADediting_1251356(18210894, +), ADediting_1251357(18210897, +), ADediting_1251358(18210906, +), ADediting_1251359(18210907, +), ADediting_1251360(18210915, +), ADediting_1251361(18210988, +), ADediting_1251362(18212026, +), ADediting_1251363(18212046, +), ADediting_1251364(18220353, +), ADediting_1251365(18220362, +), ADediting_1251366(18220363, +), ADediting_1251367(18220373, +), ADediting_1251368(18220466, +), ADediting_1251369(18220474, +), ADediting_1251370(18220501, +), ADediting_1251371(18220871, +), ADediting_1251372(18220872, +), ADediting_1251373(18220964, +), ADediting_1251374(18221007, +), ADediting_1251375(18221019, +), ADediting_1583215(18209706, +), ADediting_1583216(18210388, +), ADediting_1583217(18210570, +), ADediting_1583218(18210637, +), ADediting_1583219(18210920, +), ADediting_1583220(18210934, +), ADediting_1583221(18210955, +), ADediting_1583222(18212039, +), ADediting_1583223(18218391, +), ADediting_1583224(18220913, +), ADediting_1583225(18220934, +), ADediting_1661038(18166658, +), ADediting_1661039(18212048, +),

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RNA editing positional annotations for KDM1B 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_1251296chr6_18156715_+intronic
ADediting_1251297chr6_18156730_+intronic
ADediting_1251298chr6_18156731_+intronic
ADediting_1251299chr6_18159026_+intronic
ADediting_1251300chr6_18166590_+intronic
ADediting_1251301chr6_18166595_+intronic
ADediting_1251302chr6_18166756_+intronic
ADediting_1251303chr6_18166774_+intronic
ADediting_1251304chr6_18166779_+intronic
ADediting_1251305chr6_18166809_+intronic
ADediting_1251306chr6_18166817_+intronic
ADediting_1251307chr6_18167286_+intronic
ADediting_1251308chr6_18173866_+intronic
ADediting_1251309chr6_18173886_+intronic
ADediting_1251310chr6_18173911_+intronic
ADediting_1251311chr6_18183368_+intronic
ADediting_1251312chr6_18188877_+intronic
ADediting_1251313chr6_18188901_+intronic
ADediting_1251314chr6_18188913_+intronic
ADediting_1251315chr6_18188984_+intronic
ADediting_1251316chr6_18189019_+intronic
ADediting_1251317chr6_18189036_+intronic
ADediting_1251318chr6_18192951_+intronic
ADediting_1251319chr6_18193400_+intronic
ADediting_1251320chr6_18193406_+intronic
ADediting_1251321chr6_18193419_+intronic
ADediting_1251322chr6_18193436_+intronic
ADediting_1251323chr6_18193522_+intronic
ADediting_1251324chr6_18197981_+intronic
ADediting_1251325chr6_18197984_+intronic
ADediting_1251326chr6_18197995_+intronic
ADediting_1251327chr6_18198426_+intronic
ADediting_1251328chr6_18198438_+intronic
ADediting_1251329chr6_18198451_+intronic
ADediting_1251330chr6_18198598_+intronic
ADediting_1251331chr6_18198913_+intronic
ADediting_1251332chr6_18198973_+intronic
ADediting_1251333chr6_18198982_+intronic
ADediting_1251334chr6_18198983_+intronic
ADediting_1251335chr6_18198990_+intronic
ADediting_1251336chr6_18199051_+intronic
ADediting_1251337chr6_18199091_+intronic
ADediting_1251338chr6_18199092_+intronic
ADediting_1251339chr6_18199130_+intronic
ADediting_1251340chr6_18199158_+intronic
ADediting_1251341chr6_18199903_+intronic
ADediting_1251342chr6_18199934_+intronic
ADediting_1251343chr6_18200008_+intronic
ADediting_1251344chr6_18200071_+intronic
ADediting_1251345chr6_18200092_+intronic
ADediting_1251346chr6_18200095_+intronic
ADediting_1251347chr6_18210461_+intronic
ADediting_1251348chr6_18210470_+intronic
ADediting_1251349chr6_18210596_+intronic
ADediting_1251350chr6_18210600_+intronic
ADediting_1251351chr6_18210621_+intronic
ADediting_1251352chr6_18210623_+intronic
ADediting_1251353chr6_18210624_+intronic
ADediting_1251354chr6_18210743_+intronic
ADediting_1251355chr6_18210774_+intronic
ADediting_1251356chr6_18210894_+intronic
ADediting_1251357chr6_18210897_+intronic
ADediting_1251358chr6_18210906_+intronic
ADediting_1251359chr6_18210907_+intronic
ADediting_1251360chr6_18210915_+intronic
ADediting_1251361chr6_18210988_+intronic
ADediting_1251362chr6_18212026_+intronic
ADediting_1251363chr6_18212046_+intronic
ADediting_1251364chr6_18220353_+intronic
ADediting_1251365chr6_18220362_+intronic
ADediting_1251366chr6_18220363_+intronic
ADediting_1251367chr6_18220373_+intronic
ADediting_1251368chr6_18220466_+intronic
ADediting_1251369chr6_18220474_+intronic
ADediting_1251370chr6_18220501_+intronic
ADediting_1251371chr6_18220871_+intronic
ADediting_1251372chr6_18220872_+intronic
ADediting_1251373chr6_18220964_+intronic
ADediting_1251374chr6_18221007_+intronic
ADediting_1251375chr6_18221019_+intronic
ADediting_1583215chr6_18209706_+intronic
ADediting_1583216chr6_18210388_+intronic
ADediting_1583217chr6_18210570_+intronic
ADediting_1583218chr6_18210637_+intronic
ADediting_1583219chr6_18210920_+intronic
ADediting_1583220chr6_18210934_+intronic
ADediting_1583221chr6_18210955_+intronic
ADediting_1583222chr6_18212039_+intronic
ADediting_1583223chr6_18218391_+intronic
ADediting_1583224chr6_18220913_+intronic
ADediting_1583225chr6_18220934_+intronic
ADediting_1661038chr6_18166658_+intronic
ADediting_1661039chr6_18212048_+intronic

check button Repat-regional RNA editing(s).
ADeditome IDPositionRepeat familyRepeat sub familyRepeat name
ADediting_1251296chr6_18156715_+SINEAluName=AluSz
ADediting_1251297chr6_18156730_+SINEAluName=AluSz
ADediting_1251298chr6_18156731_+SINEAluName=AluSz
ADediting_1251299chr6_18159026_+SINEAluName=AluSg
ADediting_1251300chr6_18166590_+SINEAluName=AluJr
ADediting_1251301chr6_18166595_+SINEAluName=AluJr
ADediting_1251302chr6_18166756_+SINEAluName=AluJr
ADediting_1251303chr6_18166774_+SINEAluName=AluJr
ADediting_1251304chr6_18166779_+SINEAluName=AluJr
ADediting_1251305chr6_18166809_+SINEAluName=AluJr
ADediting_1251306chr6_18166817_+SINEAluName=AluJr
ADediting_1251307chr6_18167286_+SINEAluName=AluSc
ADediting_1251308chr6_18173866_+SINEAluName=AluSg
ADediting_1251309chr6_18173886_+SINEAluName=AluSg
ADediting_1251310chr6_18173911_+SINEAluName=AluSg
ADediting_1251311chr6_18183368_+SINEAluName=AluSq2
ADediting_1251312chr6_18188877_+SINEAluName=AluSz
ADediting_1251313chr6_18188901_+SINEAluName=AluSz
ADediting_1251314chr6_18188913_+SINEAluName=AluSz
ADediting_1251315chr6_18188984_+SINEAluName=AluSz
ADediting_1251316chr6_18189019_+SINEAluName=AluSz
ADediting_1251317chr6_18189036_+SINEAluName=AluSz
ADediting_1251318chr6_18192951_+SINEAluName=AluSq2
ADediting_1251319chr6_18193400_+SINEAluName=AluJo
ADediting_1251320chr6_18193406_+SINEAluName=AluJo
ADediting_1251321chr6_18193419_+SINEAluName=AluJo
ADediting_1251322chr6_18193436_+SINEAluName=AluJo
ADediting_1251323chr6_18193522_+SINEAluName=AluJo
ADediting_1251324chr6_18197981_+SINEAluName=AluSz
ADediting_1251325chr6_18197984_+SINEAluName=AluSz
ADediting_1251326chr6_18197995_+SINEAluName=AluSz
ADediting_1251327chr6_18198426_+SINEAluName=AluSz
ADediting_1251328chr6_18198438_+SINEAluName=AluSz
ADediting_1251329chr6_18198451_+SINEAluName=AluSz
ADediting_1251330chr6_18198598_+SINEAluName=AluYc
ADediting_1251331chr6_18198913_+SINEAluName=AluJb
ADediting_1251332chr6_18198973_+SINEAluName=AluJb
ADediting_1251333chr6_18198982_+SINEAluName=AluJb
ADediting_1251334chr6_18198983_+SINEAluName=AluJb
ADediting_1251335chr6_18198990_+SINEAluName=AluJb
ADediting_1251336chr6_18199051_+SINEAluName=AluJb
ADediting_1251337chr6_18199091_+SINEAluName=AluJb
ADediting_1251338chr6_18199092_+SINEAluName=AluJb
ADediting_1251339chr6_18199130_+SINEAluName=AluJb
ADediting_1251340chr6_18199158_+SINEAluName=AluJb
ADediting_1251341chr6_18199903_+SINEAluName=AluSz6
ADediting_1251342chr6_18199934_+SINEAluName=AluSz6
ADediting_1251343chr6_18200008_+SINEAluName=AluSz6
ADediting_1251344chr6_18200071_+SINEAluName=AluSz6
ADediting_1251345chr6_18200092_+SINEAluName=AluSz6
ADediting_1251346chr6_18200095_+SINEAluName=AluSz6
ADediting_1251347chr6_18210461_+SINEAluName=AluJr
ADediting_1251348chr6_18210470_+SINEAluName=AluJr
ADediting_1251349chr6_18210596_+SINEAluName=AluJr
ADediting_1251350chr6_18210600_+SINEAluName=AluJr
ADediting_1251351chr6_18210621_+SINEAluName=AluJr
ADediting_1251352chr6_18210623_+SINEAluName=AluJr
ADediting_1251353chr6_18210624_+SINEAluName=AluJr
ADediting_1251354chr6_18210743_+SINEAluName=AluJr
ADediting_1251355chr6_18210774_+SINEAluName=AluJr
ADediting_1251356chr6_18210894_+SINEAluName=AluJr
ADediting_1251357chr6_18210897_+SINEAluName=AluJr
ADediting_1251358chr6_18210906_+SINEAluName=AluJr
ADediting_1251359chr6_18210907_+SINEAluName=AluJr
ADediting_1251360chr6_18210915_+SINEAluName=AluJr
ADediting_1251361chr6_18210988_+SINEAluName=AluJr
ADediting_1251362chr6_18212026_+SINEAluName=AluSx1
ADediting_1251363chr6_18212046_+SINEAluName=AluSx1
ADediting_1251364chr6_18220353_+SINEAluName=AluSx1
ADediting_1251365chr6_18220362_+SINEAluName=AluSx1
ADediting_1251366chr6_18220363_+SINEAluName=AluSx1
ADediting_1251367chr6_18220373_+SINEAluName=AluSx1
ADediting_1251368chr6_18220466_+SINEAluName=AluSx1
ADediting_1251369chr6_18220474_+SINEAluName=AluSx1
ADediting_1251370chr6_18220501_+SINEAluName=AluSx1
ADediting_1251371chr6_18220871_+SINEAluName=AluSx
ADediting_1251372chr6_18220872_+SINEAluName=AluSx
ADediting_1251373chr6_18220964_+SINEAluName=AluSx
ADediting_1251374chr6_18221007_+SINEAluName=AluSx
ADediting_1251375chr6_18221019_+SINEAluName=AluSx
ADediting_1583215chr6_18209706_+SINEAluName=AluJr
ADediting_1583216chr6_18210388_+SINEAluName=AluJr
ADediting_1583217chr6_18210570_+SINEAluName=AluJr
ADediting_1583218chr6_18210637_+SINEAluName=AluJr
ADediting_1583219chr6_18210920_+SINEAluName=AluJr
ADediting_1583220chr6_18210934_+SINEAluName=AluJr
ADediting_1583221chr6_18210955_+SINEAluName=AluJr
ADediting_1583222chr6_18212039_+SINEAluName=AluSx1
ADediting_1583223chr6_18218391_+SINEAluName=AluJr
ADediting_1583224chr6_18220913_+SINEAluName=AluSx
ADediting_1583225chr6_18220934_+SINEAluName=AluSx
ADediting_1661038chr6_18166658_+SINEAluName=AluJr
ADediting_1661039chr6_18212048_+SINEAluName=AluSx1

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RNA A-to-I editing events in the alternative splicing sites for KDM1B

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 KDM1B

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.

check button Distribution of the averaged gene isoform expression in AD and control with or without RNA A-to-I editing event.
boxplot
boxplot
boxplot
boxplot
boxplot

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.

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 KDM1B

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 KDM1B


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

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

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

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_286380chr11_79422188_-ENSG00000165097.16ENST00000297792.9KDM1B-201hsa-miR-5579-3pchr618222977182229837mer-m81822296318222984150-9.3
ADediting_286380chr11_79422188_-ENSG00000165097.16ENST00000650836.2KDM1B-205hsa-miR-5579-3pchr618222977182229837mer-m81822296318222984150-9.3

check button Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for KDM1B

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.

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

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

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Relation with ADAR for KDM1B

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.)
DLPFCADediting_1251326chr6_18197995_+0.465951810013966-0.04155904147062450.0273900293538758-0.1252995131354063.56536517464807e-130.397441828162063
DLPFCADediting_1251327chr6_18198426_+0.524731483330913-0.03626089109262170.0210523897128856-0.1309953519301794.30044753014397e-090.325696767823698
DLPFCADediting_1251335chr6_18198990_+0.792474337880662-0.01500278093486380.0348033585438906-0.1199277412174753.3388516753045e-120.381905903162591
DLPFCADediting_1251339chr6_18199130_+0.20775665686013-0.07174704904784410.0259968012727742-0.1264459314097374.55351276872244e-080.304386522562002
DLPFCADediting_1251342chr6_18199934_+0.4791778783567350.04033701692885180.331483298681979-0.05533778208305111.00737422144564e-160.448189739422149

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.)
DLPFC1.31502508120554e-340.6221756429244441.11713661787694e-190.484804015235287.25292014732986e-060.251697992699349
AC5.87804905499264e-800.8746554789520261.67056565291491e-420.7277592754348135.6723246881936e-170.496595872618923
PCC3.21481141119804e-180.5752467923266685.3271061053021e-140.5092966889129994.02975206391519e-070.356871452781726
CER1.25062091593492e-310.7776158578034885.10314469846857e-190.6451099419612946.30855445677377e-100.477777651529392
TCX6.28553288716039e-120.5234671679096840.0736249970498990.1465024811858132.42968970274807e-080.436099835527045
FP2.83216320700832e-240.66705140917188.584862537798e-190.6000868359141494.06509030306848e-090.422952893282839
IFG1.16074226109691e-060.8059281280856351.13636350238775e-050.7580369767278940.008194709767414970.516593578134738
PG2.06436660482586e-480.8294413595776183.7301213335973e-200.6076146909330020.1259565646742360.112604808633305
STG1.71042243423383e-090.5993262291323446.82495516129923e-060.4689306884384560.004960854178067740.303819132450314

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Relation with AD stages for KDM1B

check button Correlation between AD stages and RNA editing frequency
TissueADeditomIDpositionP-valCoeff.

check button Correlation between AD stages and this gene's expression
TissueP-valCoeff.
CER4.72605344464951e-090.526800899921552
TCX1.41756940292453e-090.546007513751703

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RelatedDrugs for KDM1B

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 KDM1B

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource