Dataset Overview
RBPPUF60
Knock-MethodshRNA
RBP FamilyRRM_1
Biosample NameHepG2
Tissue TypeLiver
Biosample TypeCell line
# of Control2
# of Treat2
SpeciesHuman
Data SourceENCODE
Profile IDENCSR648BSC
PlatformHiSeq
Pubmed ID32252787

PUF60 - Target Gene Network

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

Differential Expression Genes responding to KD/KO of PUF60
Gene Mean Expr. of Control Mean Expr. of KD/KO logFC PValue FDR

Function Analysis of Target Genes of PUF60


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
chr1206557430CT0.00011SRGAP2+FALSE
chr146751578TG0.00380LRRC41-FALSE
chrX3526659CG0.00188PRKX-FALSE(AC)nSINE,Alu
chr2102484489AC0.00281MAP4K4+FALSE
chr2219146868TC0.00764PNKD,TMBIM1+,-FALSE
chr121806710TG0.00194NBPF3+FALSE
chr126801731GT0.00325HMGN2+FALSE(T)nSINE,Alu
chr285776648TC0.00765GGCX-TRUEAluSz6SINE,Alu
chr525415881TC0.00911.FALSE
chr1205686522GT0.00427NUCKS1-FALSE
chr1204095687CA5.97770E-05SOX13+FALSE
chr417802955TC0.00071DCAF16-FALSEAluSzSINE,Alu
chr145976220AG0.00031MMACHC+TRUE
chr1953914411AG8.16883E-05ZNF765+TRUEAluSxSINE,Alu
chr11647871TC7.46571E-06CDK11B,CDK11A-FALSE
chr3191114266TC0.00258CCDC50+FALSE
chr136642420TC0.00358MAP7D1+FALSE
chr417802890TC0.00303DCAF16-TRUEAluSzSINE,Alu
chr163207362AT1.09222E-05.FALSE
chr136067886TC0.00786PSMB2-TRUEAluSzSINE,Alu
chr47762356GA3.36293E-10AFAP1,AFAP1-AS1+,-FALSE
chr11252510TC1.62601E-05CPSF3L-TRUEAluSpSINE,Alu
chr132373831TG0.00252PTP4A2-FALSE(T)nSINE,Alu
chr1610624953TC0.00056EMP2-TRUEAluSx3SINE,Alu
chr123884661GA0.00205ID3-FALSE
chr1958374130CT0.00124ZNF587+FALSE
chr274332840GC4.77205E-06TET3+FALSE
chr1610623553TC0.00024EMP2-TRUEAluSpSINE,Alu
chr7152343700TC0.00061XRCC2-TRUEAluSx3SINE,Alu
chr631321883GA0.00000.FALSE
chr631322980CT0.00091.FALSE
chr4120979190TC0.00970.FALSEAluSg4SINE,Alu
chr11534826CT0.00382FNDC10-FALSE
chr3183900729TC0.00074AP2M1+FALSEMIR3SINE,Alu
chr330733403AT0.00110TGFBR2+FALSE(TA)nSINE,Alu
chr136068237TC0.00150PSMB2-TRUEAluScSINE,Alu
chr116576836AG0.00885FBXO42-FALSE
chr136522615AG0.00658.FALSEAluScSINE,Alu
chr138327700TC0.00510INPP5B-TRUEAluSx3SINE,Alu
chr1116943511TC0.00236ATP1A1,ATP1A1-AS1+,-FALSE
chr28823941GA0.00053ID2+FALSE
chr165898873GC0.00530LEPR,LEPROT+FALSE
chr1179829425TC1.55944E-05TOR1AIP2-TRUEAluJrSINE,Alu
chr110517486TC0.00626.FALSEAluSx1SINE,Alu
chr11252662TC0.00235CPSF3L-TRUEAluSpSINE,Alu
chr1753239140CT0.00954STXBP4+FALSEMIRSINE,Alu
chr1778921108GA0.00065RPTOR+FALSE
chr541919747CT0.00814C5orf51+FALSEL2cSINE,Alu
chr1120572572CT0.00084NOTCH2-FALSE
chr1145284175GC0.00481NBPF20,NOTCH2NL+FALSE
chr159148136TC0.00244MYSM1-FALSE
chr568738649AT0.00716.FALSE
chr8143352528AC0.00312TSNARE1-FALSE
chr136067858GA0.00293PSMB2-FALSEAluSzSINE,Alu
chr110520588TC0.00341.FALSEAluSc8SINE,Alu
chr119543457TC0.00718LOC101927895,EMC1+,-FALSEAluJbSINE,Alu
chr1224380757AG0.00618DEGS1+FALSEAluSxSINE,Alu
chr1423300663GA0.00120MRPL52+FALSEMIRbSINE,Alu
chr3179117266TC0.00111GNB4-TRUEAluSzSINE,Alu
chr317202334AC0.00770TBC1D5-FALSE
chr549692633TG0.00808EMB-FALSE
chr1269158881AG0.00219SLC35E3+TRUEAluSpSINE,Alu
chr1179044181AG0.00790FAM20B+TRUEAluSxSINE,Alu
chr2191745643AC0.00011GLS+FALSE(GCA)nSINE,Alu
chr2218572729AG0.00228PEX26+TRUEAluYf1SINE,Alu
chr14103372465CA0.00600TRAF3+FALSE(AC)nSINE,Alu
chr1174551853AC0.00079RNF169+FALSE
chr3196729939CT0.00862MELTF,MFI2-AS1+,-FALSEG-richSINE,Alu
chr2176792536GT0.00211LNPK-FALSE
chr110517992TC0.00417.FALSEAluJrSINE,Alu
chr116893691CA0.00371NBPF1-FALSE
chr12115914GT0.00970PRKCZ,FAAP20+,-FALSE
chr642856156AG0.00190RPL7L1+TRUEAluSzSINE,Alu
chr12161135AG0.00028SKI+FALSE
chr135658211GT1.28982E-07SFPQ-FALSE
chr1197073932TC0.00032ASPM-FALSE
chr1145281613CA0.00979NBPF20,NOTCH2NL+FALSE
chr1256215103AT0.00353DNAJC14-FALSE
chr3160213317TA0.00208KPNA4-FALSE
chr136068370TC0.00067PSMB2-TRUEAluScSINE,Alu
chr579279310TA0.00173MTX3-FALSE
chr1760522252GA0.00187METTL2A+FALSE
chr439550549TC0.00014UGDH-AS1,SMIM14+,-FALSEAluSx1SINE,Alu
chr133148736AG4.97736E-05SYNC,RBBP4+,-FALSEAluScSINE,Alu
chr121793735CG0.00099NBPF3+FALSE
chr8133859871TA0.00027PHF20L1+FALSE
chr110517623TC0.00348.FALSEAluSx1SINE,Alu
chr136068369TC0.00012PSMB2-TRUEAluScSINE,Alu
chr16259025CT0.00700RPL22-FALSE
chr133148740AG0.00210SYNC,RBBP4+,-FALSEAluScSINE,Alu
chr225962253AT0.00784ASXL2-FALSE
chr193827995CT0.00714DR1+FALSE
chr7128607384GA0.00925TNPO3-FALSE
chr144088547CA0.00927PTPRF+FALSEA-richSINE,Alu
chr112071680AG5.54475E-07MFN2+FALSE
chr1144931392GA0.00172NBPF20,PDE4DIP+,-FALSE
chr9131872862CG0.00131CRAT-FALSE
chr674493432AC0.00611CD109+FALSE
chr339452123GA0.00093RPSA+FALSE
chr136770065CT0.00131THRAP3+FALSE(T)nSINE,Alu
chr136529419AG0.00842.FALSEAluJrSINE,Alu
chr393780109GC8.09346E-05DHFR2-FALSE
chr1156565049AC0.00169GPATCH4-FALSE
chr11650797AG0.00276CDK11B,CDK11A-FALSE
chr572801321TA0.00212BTF3+FALSE
chr124798068CA0.00686NIPAL3+FALSEAluJrSINE,Alu
chr7131241052AG0.00663PODXL-FALSE(GGCGAC)nSINE,Alu
chr110517672TC0.00070.FALSEAluSx1SINE,Alu
chr1204525667AG3.94227E-05MDM4+TRUEAluSzSINE,Alu
chr1011912065CG0.00191PROSER2-AS1,PROSER2+,-FALSE
chr1610623576TC0.00013EMP2-TRUEAluSpSINE,Alu
chr185786957TG0.00959DDAH1-FALSE
chr140537944CA2.58277E-05CAP1+FALSE
chr6150047376TC0.00102NUP43-TRUEAluScSINE,Alu
chr314985983AT6.81677E-14FGD5-AS1-FALSE
chr574063154CG0.00255GFM2,NSA2+,-FALSE
chr250147867TA0.00896NRXN1-FALSE(GT)nSINE,Alu
chr4119555142AG4.95460E-05LOC729218+FALSE
chr1201488170AG0.00997.FALSEAluSzSINE,Alu
chr35257975AT9.78592E-05EDEM1+FALSE
chr895805071AG1.12730E-06DPY19L4+TRUEAluYf1SINE,Alu
chrM5265CA0.00026.FALSE
chr12124146094AG2.86040E-06GTF2H3+TRUEAluSx4SINE,Alu
chr1229730452GA0.00236TAF5L-FALSE
chr133148691AG0.00032SYNC,RBBP4+,-FALSEAluScSINE,Alu
chr1179852074TC0.00033TOR1AIP1+FALSE
chr145279903CT0.00052.FALSE(TCTT)nSINE,Alu
chr6114182271GA0.00011MARCKS+FALSE
chr193617406AT0.00275TMED5-FALSE
chr123636028TA0.00029HNRNPR-FALSE
chr116893822CT0.00808NBPF1-FALSE
chr146075191CA0.00457NASP+FALSEA-richSINE,Alu
chr1179326418AG0.00626SOAT1+TRUEAluSgSINE,Alu
chr968413593CA0.00342.FALSE
chr110520331CT2.36721E-05.FALSEAluSx1SINE,Alu
chr344791343TC0.00220KIAA1143-FALSEAluJrSINE,Alu
chr1264842974CA0.00925.FALSEAluSzSINE,Alu
chr11345051AG0.00362.FALSEAluSgSINE,Alu
chr261277443AG0.00362PEX13+TRUEAluSxSINE,Alu
chr47762313CG5.86540E-10AFAP1,AFAP1-AS1+,-FALSE
chr5151041886TG0.00176SPARC-FALSE
chr167518534CT0.00682SLC35D1-FALSE
chr3155658362CT0.00807.FALSEMIR3SINE,Alu
chr16282255TC0.00954ICMT-TRUEAluSzSINE,Alu
chr399517466GA0.00088MIR548G-FALSE(TG)nSINE,Alu
chr191990450AT0.00091CDC7+FALSELFSINE_VertSINE,Alu
chr1666765441GT4.44089E-16DYNC1LI2-FALSEL2cSINE,Alu
chr3186505900TG1.87786E-07EIF4A2+FALSE
chr116958047CT0.00193.FALSE
chr42940486TC7.87098E-05NOP14-AS1,NOP14+,-FALSEAluJoSINE,Alu
chr115993013GA1.16652E-10.FALSE
chr1120162635AT0.00203ZNF697-FALSE
chr3195243023AC0.00729PPP1R2-FALSE
chr273460310GC0.00091PRADC1-FALSE(CGGCGC)nSINE,Alu
chr1184663581TC0.00265EDEM3-FALSE
chr1155030557AC0.00883LOC100505666,ADAM15+,-FALSE
chr145975345AG0.00357MMACHC+TRUEAluSg7SINE,Alu
chr1157963369CG0.00667KIRREL+FALSE
chr1151095753AG0.00256GABPB2+TRUEAluSzSINE,Alu
chr1765334886TC8.05380E-09PSMD12-TRUEAluSqSINE,Alu
chr1156256064CT0.00619SMG5,TMEM79+,-FALSE
chr1220232144TC1.06602E-07RNU5F-1,BPNT1+,-FALSEAluSzSINE,Alu
chr45710647AG5.78692E-06EVC2-FALSE
chr19161550GA0.00043.FALSE
chr11419130AG0.00107ATAD3B+FALSEAluSzSINE,Alu
chr1149581854CA0.00175LINC00623,LINC00869,LOC103091866+FALSEL2bSINE,Alu
chr11469787CT0.00010ATAD3A+FALSE
chr1145688682AC0.00468NBPF20,NBPF10,RNF115+FALSE
chr337366459CA2.94197E-05GOLGA4+FALSE
chr2120021785TC0.00751STEAP3+FALSE
chr2176791181TC0.00063LNPK-TRUEMSTDSINE,Alu
chr1179326295AG0.00035SOAT1+TRUE
chr1590819619AG5.14004E-06.FALSEAluSxSINE,Alu
chr454244053GC0.00726FIP1L1+FALSE(CGGAG)nSINE,Alu
chr1169480680TC0.00252ORAOV1-FALSEAluSx1SINE,Alu
chr286249930TC6.06022E-05LOC90784-TRUEAluJrSINE,Alu
chr1256215102TA0.00405DNAJC14-FALSE
chr270677439AG0.00498TGFA-FALSE
chr1741133089CT0.00179RUNDC1+FALSE
chr1146740502CG0.00692CHD1L+FALSE
chr1774555106TC0.00164SNHG16+FALSE
chr2175711942CT8.43847E-05CHN1-FALSE
chr7131241049GA0.00145PODXL-FALSE(GGCGAC)nSINE,Alu
chr1121134169AT0.00660SRGAP2-AS1,SRGAP2B,SRGAP2C+,-FALSE(TTTCCT)nSINE,Alu
chr697592897AC0.00144MMS22L-FALSE
chr232535836AG0.00163.FALSEAluJbSINE,Alu
chr186817074GT9.65311E-06ODF2L-FALSEL1PA7SINE,Alu
chr1689630630CT0.00296RPL13+FALSE
chr264069566AG0.00075UGP2+FALSE
chr116478619GA0.00656TRIM3-FALSE
chr350686350TG2.12445E-05MAPKAPK3+FALSE
chr2174086940CA0.00047ZAK,MLK7-AS1+,-FALSEAluJoSINE,Alu
chr11595388AG0.00135CDK11B,SLC35E2B-FALSEAluJrSINE,Alu
chr1148251079TC0.00880NBPF8,NBPF14,NBPF9-FALSEL1MC4SINE,Alu
chr1176132119GC0.00134RFWD2-FALSEL3bSINE,Alu
chr110521238TC0.00173DFFA-TRUEAluYSINE,Alu
chr1200375837TG0.00490ZNF281-FALSE(T)nSINE,Alu
chr162164735CT0.00016TM2D1-FALSEAluJbSINE,Alu
chr237330611TC0.00835.FALSEAluSq2SINE,Alu
chr1160966352TC1.19601E-07F11R-TRUEAluSgSINE,Alu
chr4178256913CG4.41796E-05NEIL3+FALSE
chr146075777AG0.00268NASP+TRUEAluSx4SINE,Alu
chr1156613632GA0.00187BCAN+FALSE
chr1071993094TG0.00078PPA1-FALSE
chr2196600548GT0.00036SLC39A10+FALSE
chr744841237TA0.00599PPIA+FALSE
chr2172178588TC0.00369METTL8-TRUEAluSx3SINE,Alu
chr285132772GC5.10736E-05TMSB10+FALSE
chr12125512540AG7.43833E-09.FALSE
chr1574319733AG0.00524PML+TRUEAluJrSINE,Alu
chr5151041876GT5.29152E-05SPARC-FALSE
chr652860422GC0.00024.FALSE7SKSINE,Alu
chr1205737659CT0.00024RAB29-FALSEAluSq2SINE,Alu
chr19161142TC8.95302E-05.FALSEAluSxSINE,Alu
chr3194789330GT0.00699XXYLT1-FALSEAluJrSINE,Alu
chr1145689271AG0.00250NBPF20,NBPF10+FALSE
chr556177872AG0.00618MAP3K1+TRUE(CAA)nSINE,Alu
chr132661578CT0.00623TXLNA+FALSE(T)nSINE,Alu
chr229135468CG0.00262WDR43+FALSE
chr579276281AG0.00026MTX3-FALSE
chr145975358AG0.00020MMACHC+TRUEAluSg7SINE,Alu
chr2025428588AG0.00068GINS1+TRUEAluJbSINE,Alu
chr1156564754AG0.00562GPATCH4-FALSE
chr1179829401TC0.00118TOR1AIP2-TRUEAluJrSINE,Alu
chr153291408AG0.00931ZYG11B+TRUEAluJrSINE,Alu
chr153716416GA0.00967LRP8-FALSE
chr116889639TC0.00350NBPF1-TRUE
chr1161931167AG0.00251ATF6+FALSE
chr14105270483GT7.92193E-06ZBTB42+FALSE
chr119543352TC0.00279LOC101927895,EMC1+,-FALSEAluJbSINE,Alu
chr1227848051CA0.00245PPFIBP1+FALSE
chr11152309AT0.00035SDF4-FALSE
chr6150046603TC0.00730NUP43-TRUEAluSq2SINE,Alu
chr2206987738TC0.00859.FALSEAluJbSINE,Alu
chr116893686GC0.00171NBPF1-FALSE
chr9124094999GT0.00764GSN+FALSE(TG)nSINE,Alu
chr439549693TC0.00170UGDH-AS1,SMIM14+,-FALSEAluSpSINE,Alu
chr116935130CT0.00155NBPF1-FALSE
chr110042987AG0.00149NMNAT1+TRUEAluScSINE,Alu
chr1675479484TC1.12347E-07TMEM170A-TRUEAluJbSINE,Alu
chr124286327GA0.00053PNRC2+FALSE
chr1113672640AG0.00629.FALSEAluJbSINE,Alu
chr1211918115CT7.42155E-06LPGAT1-FALSEMER63DSINE,Alu
chr1681744038TC6.34278E-05CMIP+FALSE(CCGC)nSINE,Alu
chr2029631557AG0.00159FRG1BP+FALSE
chr18931947TC0.00059ENO1-FALSE
chr133148698AG0.00736SYNC,RBBP4+,-FALSEAluScSINE,Alu
chr12133298339AG1.45756E-07PGAM5+TRUEAluSpSINE,Alu
chr690344605TC0.00013LYRM2-TRUEAluSz6SINE,Alu
chr210580506AT0.00294ODC1-FALSE
chr2136541072TC0.00496UBXN4+FALSE
chr136067677TC1.65353E-05PSMB2-TRUEAluSzSINE,Alu
chr3183861243AG0.00049EIF2B5+FALSE
chr3197611291AG0.00095.FALSEAluSx1SINE,Alu
chr422404391GA0.00338ADGRA3-FALSE
chr4129795661AT0.00165JADE1+FALSE
chr729961939GT1.47033E-05SCRN1-FALSE
chr116889413TC8.21040E-06NBPF1-TRUEL1MC4SINE,Alu
chr159121768GC0.00196MYSM1-FALSE
chr126673076GA0.00465AIM1L-FALSE
chr119585493AG3.52757E-05MRTO4+TRUEAluSc8SINE,Alu
chr199672346TC0.00222.FALSEAluJrSINE,Alu
chr146075604AG0.00155NASP+TRUEAluSx4SINE,Alu
chr110044367AG5.42058E-05NMNAT1+TRUEAluSx1SINE,Alu
chr1206566948GA0.00228SRGAP2+FALSE
chr5130538076AG0.00045LYRM7+TRUEAluSpSINE,Alu
chr1254526562AT0.00119LOC400043+FALSEL2aSINE,Alu
chr174929000AG0.00214KIF1C+TRUEAluYSINE,Alu
chr42940098TC0.00034NOP14-AS1,NOP14+,-FALSEAluSpSINE,Alu
chr3122447574AC0.00224PARP14+FALSE
chr810689212CT3.39921E-05PINX1-FALSE

Differential Expression Gene Analysis