Dataset Overview
RBPYBX3
Knock-MethodshRNA
RBP FamilyCSD
Biosample NameK562
Tissue TypeHaematopoietic_and_lymphoid_tissue
Biosample TypeCell line
# of Control2
# of Treat2
SpeciesHuman
Data SourceENCODE
Profile IDENCSR306EIU
PlatformHiSeq
Pubmed ID32252787

YBX3 - Target Gene Network

up-regulated gene   
down-regulated gene   
Gene Type: # of Top Genes:

Differential Expression Genes responding to KD/KO of YBX3
Gene Mean Expr. of Control Mean Expr. of KD/KO logFC PValue FDR

Function Analysis of Target Genes of YBX3


Differential Alternative Splicing
  • Exon Skipping
  • Mutually Exclusive Exons
  • Alternative 5’ splice site
  • Alternative 3’ splice site
  • Intron Retention
RBP LongES_LongEE_ShortES_ShortEE_FlankingES_FlankingEE pValue △Inc Dataset ID Sashimi plot
RBP LongES_LongEE_ShortES_ShortEE_FlankingES_FlankingEE pValue △Inc Dataset ID Sashimi plot
RBP LongES_LongEE_ShortES_ShortEE_FlankingES_FlankingEE pValue △Inc Dataset ID Sashimi plot
RBP LongES_LongEE_ShortES_ShortEE_FlankingES_FlankingEE pValue △Inc Dataset ID Sashimi plot
RBP LongES_LongEE_ShortES_ShortEE_FlankingES_FlankingEE pValue △Inc Dataset ID Sashimi plot

Differential Variants in RNA (DVRs)
Chrom Site Ref_allele Alt_allele Pvalue Genename Strand KnownRNAediting RepeatName RepeatFamily
chr345721891AG0.00163LIMD1,LIMD1-AS1+,-FALSEAluJbSINE,Alu
chr344791398TC0.00204KIAA1143-TRUEAluJrSINE,Alu
chr1765335477TC2.02482E-05PSMD12-TRUEAluSxSINE,Alu
chr1572635829AC0.00054HEXA-FALSE
chr633648144CT0.00453ITPR3+FALSE
chr133086834TC0.00251ZBTB8OS-TRUEAluYSINE,Alu
chr312625747GA0.00067RAF1-FALSE
chr128662212AG0.00098MED18+TRUEAluSq2SINE,Alu
chr126161104CA0.00030AUNIP-FALSEAluSc8SINE,Alu
chr1212277618TG0.00173DTL+FALSE
chr1075008817TC1.29877E-10DNAJC9-AS1,MRPS16+,-FALSEAluJrSINE,Alu
chr525415881TC0.00911.FALSE
chr2185802243CA0.00172ZNF804A+FALSE
chr189299658GA0.00779PKN2+FALSE
chr119543465TC0.00117LOC101927895,EMC1+,-FALSEAluJbSINE,Alu
chr1118502684GA0.00682WDR3,SPAG17+,-FALSE
chr1145293515AG4.09953E-06NBPF20,NBPF10+FALSE
chr3196670082AT0.00261NCBP2-AS2+FALSE
chr116894514CT0.00270NBPF1-FALSE
chr274690039GA0.00412MOGS-FALSE
chr2242291743AG0.00731SEPT2+FALSE
chr119542464TC0.00140LOC101927895,EMC1+,-FALSEAluSzSINE,Alu
chr2217366192TA0.00067.FALSE
chr271214819AT0.00346TEX261-FALSE
chr340503729AG5.91625E-05RPL14+FALSE
chr56372180CT0.00034MED10-FALSE
chr136067760TC0.00024PSMB2-TRUEAluSzSINE,Alu
chr1117910682GA0.00013MAN1A2+FALSE
chr12125514122AG1.22592E-05.FALSE(TA)nSINE,Alu
chr151434560GA6.87938E-05CDKN2C+FALSE
chr237329214TC0.00081.FALSEAluJr4SINE,Alu
chr350686350TG2.12445E-05MAPKAPK3+FALSE
chr186049389TA0.00420CYR61+FALSE
chr12133298125AG0.00025PGAM5+TRUEAluJoSINE,Alu
chr1145689568AG0.00131NBPF20,NBPF10+TRUEAluSgSINE,Alu
chr720177613TC0.00913MACC1,LOC101927668-TRUEAluSxSINE,Alu
chrX77083614TC6.82446E-05MAGT1-TRUEAluSz6SINE,Alu
chr4128756632AG0.00602.FALSEAluSxSINE,Alu
chr1542550349AC0.00120TMEM87A-FALSE
chr133148365GC0.00062SYNC,RBBP4+,-FALSEAluSgSINE,Alu
chr7300512GA3.09252E-06FAM20C+FALSE
chr1120163247TC0.00365ZNF697-FALSE
chr119545147TG0.00510LOC101927895,EMC1+,-FALSE
chr1150704486TC0.00947CTSS-TRUEAluJoSINE,Alu
chr16583097TC0.00022NOL9-TRUEAluSx4SINE,Alu
chr1155582104TA0.00099MSTO1+FALSE
chr4178256913CG4.41796E-05NEIL3+FALSE
chr145976265AG0.00657MMACHC+FALSE
chr1111489899CA0.00041LRIF1-FALSE
chr1326499AG0.00583.FALSE
chr1212515613CT0.00286PPP2R5A+FALSE
chr227279013AG6.08626E-07AGBL5+FALSE
chr596429362AT0.00907LIX1-FALSE
chr339450156AG0.00985RPSA+FALSE
chr556177845AT0.00420MAP3K1+FALSE
chr1757279257AG0.00077PRR11+TRUEAluSq2SINE,Alu
chr1206566195CT0.00052SRGAP2+FALSE
chr1274934944AG0.00094ATXN7L3B+FALSE
chrX77083617TC3.46806E-05MAGT1-TRUEAluSz6SINE,Alu
chr119542631TC0.00741LOC101927895,EMC1+,-FALSEFRAMSINE,Alu
chr1158067060TA0.00114KIRREL+FALSE
chr116889339CT0.00129NBPF1-FALSEL1MC4SINE,Alu
chr1146495577TA0.00072LOC728989-FALSE
chr2183643905AT0.00113DNAJC10+FALSE
chr126801762GT0.00762HMGN2+FALSE
chr3183900836GA2.54977E-05AP2M1+FALSE
chr1114938105TA0.00430TRIM33-FALSE
chr1669338754TC0.00210SNTB2+FALSEAluJrSINE,Alu
chr1146400122CG0.00039NBPF20,NBPF10,NBPF25P,NBPF12+FALSE
chr3149459413CT0.00097COMMD2-FALSE
chr1169468187GT0.00827CCND1+FALSE(T)nSINE,Alu
chr2217366803AG0.00914.FALSEAluSz6SINE,Alu
chr1168523016TC0.00016CPT1A-TRUEAluYSINE,Alu
chr140537941AC0.00216CAP1+FALSE(A)nSINE,Alu
chr675797290TA0.00147COL12A1-FALSE
chr1200375005AT0.00202ZNF281-FALSE
chr1567557AG0.00649.FALSE
chr11337841CA0.00186MRPL20-FALSE
chr1206669958GA0.00347IKBKE+FALSE
chr348787094TC0.00518PRKAR2A-TRUEAluSx3SINE,Alu
chr1210761846AG0.00224MAGOHB-FALSE
chr11717439TA0.00663GNB1-FALSE
chr194342564CA0.00098DNTTIP2-FALSE
chr2191745643AC0.00011GLS+FALSE(GCA)nSINE,Alu
chr112677549TA1.84464E-05DHRS3-FALSE(A)nSINE,Alu
chr1110913120CT0.00627SLC16A4-FALSE
chr192977228TC0.00206EVI5-TRUEAluJrSINE,Alu
chr116889563CA0.00090NBPF1-FALSE
chr1202821382TC0.00983.FALSEAluJrSINE,Alu
chr1109474776AG0.00088GPSM2,CLCC1+,-FALSEAluSzSINE,Alu
chr457801196GA0.00485REST+FALSE
chr126449340GA0.00711PDIK1L+FALSE
chr2236677551TC7.06365E-05MYH9-FALSE
chr165297861TC0.00895RAVER2+FALSE
chr115989141CG0.00677.FALSE
chr140539211AT0.00105PPT1-FALSE
chr1120162587GA0.00730ZNF697-FALSE
chr5149363214AG6.58903E-07SLC26A2+TRUEAluJrSINE,Alu
chr1242011534AG0.00248EXO1+FALSE
chr2232576431TC0.00593PTMA+FALSE
chr717384887AG4.32861E-08AHR+TRUEAluScSINE,Alu
chr211323079TA0.00586ROCK2-FALSE(TA)nSINE,Alu
chr2206986245TC0.00304.FALSEAluSzSINE,Alu
chr1847920424AG0.00000SKA1+FALSEMER21CSINE,Alu
chr2238484068TC0.00047RAB17-FALSE
chr111979809AC0.00836KIAA2013-FALSE
chr1773773311TG0.00474H3F3B-FALSE
chr128835847AG0.00553SNHG3,RCC1+TRUEAluSx4SINE,Alu
chr2035410314TC0.00602SOGA1-TRUEAluSzSINE,Alu
chr116890500GA0.00030NBPF1-FALSE
chr4177252326AG2.59441E-08SPCS3+TRUE
chr581571271TG0.00827RPS23-FALSE
chr1939433139TG0.00235FBXO17-FALSEAluJbSINE,Alu
chr245640374CA0.00578SRBD1-FALSE
chr468483804AT0.00720UBA6-FALSE
chr8144940792GC9.20360E-05EPPK1-FALSE
chr626096636AG0.00531.FALSEAluSgSINE,Alu
chr1144868170CT0.00750NBPF20,PDE4DIP+,-FALSE
chr1453243411TC0.00028GNPNAT1-TRUEAluSx3SINE,Alu
chr1160967856TC0.00116F11R-TRUEAluSpSINE,Alu
chr145280426AG0.00802.FALSEAluSxSINE,Alu
chr2134728175AG6.62284E-07IFNAR1+TRUEAluScSINE,Alu
chr1110951224AG0.00352LAMTOR5-AS1+TRUEAluJrSINE,Alu
chr19326888TC0.00887H6PD+FALSEAluSx1SINE,Alu
chr116890176AC0.00753NBPF1-FALSE
chr1959093999AG0.00018CENPBD1P1+TRUEAluYSINE,Alu
chr1163724398TC0.00664NAA40+FALSEAluSxSINE,Alu
chr1269237056AG0.00372MDM2+TRUE
chr1171943768GT1.87744E-06INPPL1+FALSE
chr119542239TC0.00038LOC101927895,EMC1+,-FALSEAluSzSINE,Alu
chr138174987TC0.00032CDCA8+FALSE
chr110517550TC0.00457.FALSEAluSx1SINE,Alu
chr7158590740AT0.00211ESYT2-FALSE
chr351738256AG0.00312TEX264+FALSE
chr1326539AG0.00450.FALSE
chr1253435276TG4.45732E-05EIF4B+FALSE
chr1154989595TC0.00264ZBTB7B+FALSE
chr42951804AG7.08227E-08NOP14-AS1,NOP14+,-FALSE
chr135817023GC0.00030ZMYM4+FALSE
chr119633555GA0.00219AKR7A2-FALSE
chr110519947TC0.00328.FALSEAluJrSINE,Alu
chr7115898442GC2.36867E-05TES+FALSEAluSxSINE,Alu
chr473923605TC0.00366COX18-TRUEAluSq2SINE,Alu
chr165298626TA0.00580RAVER2+FALSEX12_DNASINE,Alu
chr1179326295AG0.00035SOAT1+TRUE
chr110043363AG0.00429NMNAT1+TRUEAluSx3SINE,Alu
chr16283264TC0.00095ICMT-TRUEAluSx3SINE,Alu
chr657034840TG0.00581ZNF451,LOC101927211+,-FALSE
chr116889413TC1.64789E-05NBPF1-TRUEL1MC4SINE,Alu
chr1145695329AG0.00400NBPF20,NBPF10+FALSEAluSzSINE,Alu
chr13545184GT0.00347TPRG1L+FALSE
chr1144828764GT0.00976NBPF20,NBPF9+FALSE
chr517276078CA0.00011BASP1+FALSE(TC)nSINE,Alu
chr2217366194CA0.00359.FALSE
chr167874689TC0.00896SERBP1-TRUEAluSx3SINE,Alu
chr19162933CT0.00088.FALSE
chr125688276AG0.00187TMEM50A+FALSE
chr1419685015CG0.00069DUXAP10+FALSE
chr239212565TG0.00662SOS1-FALSE
chr11653093AG0.00642CDK11B,CDK11A-FALSEL2SINE,Alu
chr1110551680CT0.00415AHCYL1+FALSE
chr12133298349AG0.00000PGAM5+TRUEAluSpSINE,Alu
chr286731290TC0.00149CHMP3,RNF103-CHMP3-FALSEL1MC1SINE,Alu
chr3150262004AT0.00167SERP1-FALSE
chr358304244GA0.00560RPP14+FALSEAluSzSINE,Alu
chr3179117241TC0.00133GNB4-TRUEAluSzSINE,Alu
chr4129924977CA0.00760SCLT1-FALSE
chr1171561203TG0.00075PRRC2C+FALSE
chr362189465CT2.69664E-05PTPRG+FALSE
chr589820984TC0.00921LYSMD3-FALSE
chr1148556726GT0.00023.FALSE
chr133147942AG0.00423SYNC,RBBP4+,-FALSEAluSxSINE,Alu
chr764435685AT0.00239ZNF117-FALSE
chr116889041CT0.00429NBPF1-FALSE
chr5139680027AG0.00155PFDN1-FALSE
chr1155853219AG0.00520SYT11+TRUEAluJbSINE,Alu
chr237329307TC0.00201.FALSEAluJr4SINE,Alu
chr16282371TC0.00054ICMT-TRUEAluSzSINE,Alu
chr6109784327TC0.00854MICAL1,ZBTB24-TRUEAluSgSINE,Alu
chr154691922TA0.00067SSBP3-FALSE
chr145975574AG0.00890MMACHC+TRUEAluSx4SINE,Alu
chr1228682330CG0.00509RNF187+FALSE
chr1145512944AG0.00171NBPF20,NBPF10,RBM8A,GNRHR2+,-FALSEAluSz6SINE,Alu
chr153292607TA2.07283E-05ZYG11B+FALSE
chr1911257673TC0.00155SPC24-TRUEAluSpSINE,Alu
chr125893932TC0.00866LDLRAP1+FALSE
chr457326313AG0.00132PAICS+TRUEAluJrSINE,Alu
chr1220231370TC0.00826RNU5F-1,BPNT1+,-FALSEAluYSINE,Alu
chr9116022896TC9.26547E-05SLC31A1+FALSE
chr194353045GT0.00351GCLM-FALSEAluSgSINE,Alu
chr110517952CA0.00341.FALSE
chr67310259AG0.00092SSR1-FALSE
chr119586520AG0.00659MRTO4+TRUEAluSzSINE,Alu
chr690346418AT1.30335E-05LYRM2-FALSEAluSzSINE,Alu
chr145975345AG0.00273MMACHC+TRUEAluSg7SINE,Alu
chr310193797AG0.00261VHL+TRUEAluSxSINE,Alu
chr19811933CT0.00026PTBP1+FALSE
chr16582353TC0.00121NOL9-TRUEAluSx1SINE,Alu
chr537290571TC0.00097.FALSEAluSzSINE,Alu
chr155316322AG0.00172DHCR24-FALSE
chr136534736AG0.00016.FALSEAluJoSINE,Alu
chr112073251GT0.00957MFN2+FALSE
chr1657505662TG0.00332POLR2C+FALSE(GGTGGG)nSINE,Alu
chr128920944AG0.00446RAB42+TRUEAluSxSINE,Alu
chr345721990AG0.00779LIMD1,LIMD1-AS1+,-FALSEAluJbSINE,Alu
chr119542463TC0.00447LOC101927895,EMC1+,-FALSEAluSzSINE,Alu
chr175671215CT0.00019SLC44A5-FALSE
chr2239259540GA0.00493CBX6-FALSE
chr627327349CG0.00359ZNF204P-FALSE
chr2201842323TC0.00254FAM126B-TRUEAluJbSINE,Alu
chr352448770AG0.00498PHF7+TRUEAluJbSINE,Alu
chr10102308803GC0.00324HIF1AN+FALSE(GT)nSINE,Alu
chr540835311AT0.00632RPL37-FALSE
chr132373437GA1.22125E-14PTP4A2-FALSE
chr237330476TC2.74271E-05.FALSEAluSq2SINE,Alu
chr1232532505GA0.00385.FALSE
chr1156692054AT0.00471ISG20L2-FALSEAluYSINE,Alu
chr144818528TG0.00486ERI3-FALSE
chr128566320TC0.00309.FALSEAluSx1SINE,Alu
chr1450792961GA0.00547.FALSEAluSxSINE,Alu
chr119238562GA3.36880E-06IFFO2-FALSE
chr1765335253TC0.00344PSMD12-TRUEAluSxSINE,Alu
chr19331254AG0.00793H6PD+TRUEAluSxSINE,Alu
chr1145369354CT0.00872NBPF20,NBPF10+FALSE
chr345960578GA0.00632FYCO1-FALSE
chr286251114TC0.00150.FALSEAluSxSINE,Alu
chr1173864944GT2.40127E-05.FALSE
chr1171509327GA0.00110PRRC2C+FALSE
chr1160967816TC0.00162F11R-TRUEAluSpSINE,Alu
chr2238673923CA0.00813LRRFIP1+FALSE(CA)nSINE,Alu
chr1756049824TC5.91767E-06VEZF1-TRUE
chr613788222TC0.00490MCUR1-TRUEAluSxSINE,Alu
chr119586135CT0.00063MRTO4+FALSE
chr2217001882TC0.00996XRCC5+FALSE
chr1177976440CT0.00148LOC730102-FALSE
chr1109818161CT0.00840CELSR2+FALSE
chr2178406767AT0.00416AGPS+FALSE
chr4177251290GA0.00580SPCS3+FALSE
chr4156273768TC0.00058MAP9-FALSE
chr1900720AT0.00065KLHL17+FALSE(TTTA)nSINE,Alu
chr1162497663GA0.00335UHMK1+FALSE
chr320025679AG0.00292RAB5A,PP2D1+,-FALSE
chr345721891AG0.00356LIMD1,LIMD1-AS1+,-FALSEAluJbSINE,Alu
chr7131241085GA0.00600PODXL-FALSE(GCA)nSINE,Alu
chr145976262AC0.00010MMACHC+FALSE
chr1176736712AG0.00027ACER3+TRUEAluSzSINE,Alu
chr153290298AG0.00063ZYG11B+TRUEAluSg4SINE,Alu
chr119585493AG0.00199MRTO4+TRUEAluSc8SINE,Alu
chr1144340322GT0.00809NBPF20,LINC00869+,-FALSE
chr144088547CA0.00927PTPRF+FALSEA-richSINE,Alu
chr1327407AG3.55459E-07.FALSE
chr1072187740CA0.00668EIF4EBP2+FALSE
chr1241796950CA1.24743E-05OPN3,CHML-FALSE
chr19163110TC4.21626E-05.FALSEFRAMSINE,Alu
chr4170643973CT0.00232CLCN3+FALSE
chr919376248AT0.00821.FALSE
chr119585545GA0.00696MRTO4+FALSEAluSc8SINE,Alu
chr220401856TG0.00265SDC1-FALSE
chr116889985TC0.00583NBPF1-FALSE
chr1110049203GC0.00209.FALSE
chr285776832CT0.00514GGCX-FALSE
chr1533064742CG0.00215FMN1-FALSE
chr1900505GC0.00388KLHL17+FALSE
chr1574319121AG0.00311PML+TRUEAluSz6SINE,Alu
chr1226259212CA0.00167H3F3AP4,H3F3A+FALSE
chr9124095000TG0.00764GSN+FALSE(TG)nSINE,Alu
chr136068231TC9.19439E-05PSMB2-TRUEAluScSINE,Alu
chr1144930940TC6.15272E-05NBPF20,PDE4DIP+,-FALSE
chr1162354204CA0.00193C1orf226+FALSE
chr168940885GA0.00500DEPDC1-FALSEMIRSINE,Alu
chr116892277GT0.00021NBPF1-FALSE
chr287883323AG0.00910.FALSE
chr11344998AG5.29904E-05.FALSEAluSgSINE,Alu
chr3183861750AC1.09807E-05EIF2B5+FALSE
chr1236748403GC0.00519HEATR1-FALSE
chr426432834GA0.00167RBPJ+FALSE(A)nSINE,Alu

Differential Expression Gene Analysis