EuRBPDB

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TCGA tumor abbreviations
  • ACCAdrenocortical carcinoma
  • BLCABladder Urothelial Carcinoma
  • BRCABreast invasive carcinoma
  • CESCCervical squamous cell carcinoma and endocervical adenocarcinoma
  • CHOLCholangio carcinoma
  • COADColon adenocarcinoma
  • DLBCLymphoid Neoplasm Diffuse Large B-cell Lymphoma
  • ESCAEsophageal carcinoma
  • GBMGlioblastoma multiforme
  • HNSCHead and Neck squamous cell carcinoma
  • KICHKidney Chromophobe
  • KIRCKidney renal clear cell carcinoma
  • KIRPKidney renal papillary cell carcinoma
  • LAMLAcute Myeloid Leukemia
  • LGGBrain Lower Grade Glioma
  • LIHCLiver hepatocellular carcinoma
  • LUADLung adenocarcinoma
  • LUSCLung squamous cell carcinoma
  • MESOMesothelioma
  • OVOvarian serous cystadenocarcinoma
  • PAADPancreatic adenocarcinoma
  • PCPGPheochromocytoma and Paraganglioma
  • PRADProstate adenocarcinoma
  • READRectum adenocarcinoma
  • SARCSarcoma
  • SKCMSkin Cutaneous Melanoma
  • STADStomach adenocarcinoma
  • TGCTThyroid carcinoma
  • THCAThyroid carcinoma
  • THYMThymoma
  • UCECUterine Corpus Endometrial Carcinoma
  • UCSUterine Carcinosarcoma
  • UVMUveal Melanoma

Note: Click here to get the extension of tumor abbreviations.


  • Cancer Related Information
  • Basic Information

Cancer associated literatures
PIDTitleArticle TimeAuthorDoi
22741436[Association of prostate cancer with PDLIM5, SLC22A3 and NKX3-1 in Chinese men].Zhonghua Nan Ke Xue2012 MayHui J-
27350677Bayesian logistic regression in detection of gene-steroid interaction for cancer at PDLIM5 locus.J Genet2016 JunWang KS-

Differential Expression

Expression in 33 cancers

Mutations
CancerChrPosition Mutation TypedbSNPProtein-change Allele FreqRBD
ACCchr494576035Splice_SitenovelX237_splice0.34
BLCAchr494640339Nonsense_MutationnovelS391*0.18
BLCAchr494640273Splice_Regionnovel0.31
BLCAchr494455360SilentnovelF24F0.25
BLCAchr494640353Missense_MutationNAT396P0.42
BLCAchr494618093Missense_MutationnovelR337T0.21
BLCAchr494662525SilentNAC563C0.68
BLCAchr494585718Silentrs770979082Q288Q0.34
BRCAchr4946664423'UTRnovel0.07
BRCAchr494618052SilentNAT323T0.13
BRCAchr494585704Nonsense_Mutationrs772427411R284*0.3
BRCAchr494523787Missense_MutationNAD54H0.14
CESCchr494455370Missense_MutationnovelL28M0.35
CESCchr494618144Missense_MutationnovelS354F0.31
CESCchr494575754Missense_MutationnovelP144S0.12
CESCchr494657468SilentnovelC502C0.55
CESCchr494575781Missense_MutationnovelA153S0.13
CESCchr494523778Missense_MutationNAL51V0.23
CESCchr494523730Missense_MutationNAD35H0.25
CESCchr494523787Missense_MutationNAD54H0.2
COADchr494582722IntronNA0.18
COADchr494587148Intronnovel0.21
COADchr494523845Missense_MutationnovelC73Y0.09
COADchr494618072Missense_MutationnovelL330P0.36
COADchr494657483Silentrs766549570A507A0.4
COADchr494575859Missense_MutationnovelL179M0.24
COADchr494654476Missense_MutationnovelA434T0.17
COADchr494585590Missense_Mutationrs201891054R246C0.16
COADchr494579536Intronnovel0.08
COADchr494640310SilentnovelT381T0.16
COADchr494640414Missense_MutationNAR416Q0.35
COADchr494575818Missense_MutationNAP165L0.17
COADchr494587063IntronNA0.2
COADchr494585610SilentNAH252H0.42
COADchr494618086Missense_MutationNAS335A0.31
COADchr494587263Intronnovel0.25
COADchr494587265Intronnovel0.25
COADchr494523827Missense_MutationNAQ67P0.46
DLBCchr494654641Splice_SitenovelX488_splice0.23
ESCAchr494575974Missense_Mutationrs750811930S217F0.22
ESCAchr494657444SilentnovelL494L0.38
GBMchr494586425Missense_Mutationrs760060213D301N0.27
GBMchr494640414Missense_MutationNAR416Q0.36
GBMchr494585705Missense_Mutationrs755802595R284Q0.17
GBMchr494662472Nonsense_MutationnovelE546*0.05
GBMchr494455380Missense_MutationnovelS31C0.28
GBMchr494585646Frame_Shift_InsnovelI265Hfs*20.05
HNSCchr494575967Missense_MutationnovelE215K0.15
HNSCchr494455383Missense_MutationnovelS32N0.59
KIRCchr494662481Missense_Mutationrs763954536D549N0.22
KIRCchr494587083Intronnovel0.1
KIRCchr494587084Intronnovel0.08
KIRPchr494575776Missense_MutationNAT151S0.28
LIHCchr494586439SilentnovelK305K0.17
LIHCchr494618133SilentnovelK350K0.94
LIHCchr494584873Intronnovel0.46
LIHCchr494662425Missense_MutationnovelY530C0.2
LUADchr494523868Missense_MutationNAL81V0.13
LUADchr494575865Missense_MutationnovelA181S0.27
LUADchr494523841Missense_MutationnovelG72R0.44
LUADchr494523729Missense_MutationNAK34N0.21
LUADchr494618023Missense_Mutationrs778323849P314S0.17
LUADchr494523769Missense_MutationNAD48Y0.39
LUSCchr494586995Intronnovel0.14
LUSCchr494618089Missense_MutationnovelG336S0.49
LUSCchr494455329Frame_Shift_DelnovelG15Ffs*70.11
LUSCchr494587059Intronnovel0.3
LUSCchr494663987Nonsense_MutationnovelE571*0.2
LUSCchr494575938Missense_Mutationrs771478401R205Q0.37
LUSCchr494662486Missense_MutationNAM550I0.46
LUSCchr494585623Missense_MutationnovelS257G0.32
OVchr494657533Missense_MutationNAP524H0.69
OVchr494575775Missense_MutationnovelT151S0.01
PAADchr494585710Missense_MutationNAL286F0.06
PAADchr494587153Intronnovel0.14
PCPGchr494455325Missense_MutationnovelP13S0.25
PRADchr494640369Missense_MutationnovelQ401L0.11
PRADchr494455322Missense_MutationNAA12T0.1
PRADchr494640332Missense_MutationnovelA389T0.06
PRADchr494654566Missense_MutationnovelA464T0.29
READchr494618193Splice_SiteNAX370_splice0.26
READchr494584870Intronnovel0.2
READchr494640414Missense_MutationNAR416Q0.1
READchr494575845Missense_MutationnovelF174S0.4
READchr4946641243'UTRnovel0.45
SARCchr494587063IntronNA0.52
SARCchr494585689Nonsense_MutationnovelQ279*0.25
SKCMchr494585710Missense_MutationNAL286F0.22
SKCMchr494618019SilentnovelP312P0.4
SKCMchr494575713Missense_Mutationrs752588919R130Q0.38
SKCMchr494575668Missense_MutationNAS115F0.27
SKCMchr494587148Intronnovel0.5
SKCMchr494662465SilentNAF543F0.62
SKCMchr494662466Missense_MutationNAP544S0.4
SKCMchr494575889Missense_MutationNAQ189E0.06
SKCMchr494573388Nonsense_MutationNAQ96*0.29
SKCMchr494664015Missense_Mutationrs770229681S580F0.1
SKCMchr494654459Splice_SiteNAX428_splice0.39
SKCMchr494575644Missense_MutationnovelV107G0.16
SKCMchr494575985Missense_MutationNAA221T0.17
SKCMchr494654635Missense_MutationNAL487F0.64
SKCMchr494618145SilentnovelS354S0.17
SKCMchr494654635Missense_MutationNAL487F0.09
SKCMchr494587018Intronnovel0.52
SKCMchr494576007Missense_MutationNAS228F0.25
SKCMchr494575965Missense_MutationnovelS214F0.53
SKCMchr494573371Missense_MutationNAP90L0.44
STADchr494575829Missense_Mutationrs761636570V169I0.27
STADchr494585655SilentNAD267D0.09
STADchr494657455Missense_Mutationrs762186735W498S0.09
STADchr494575694Missense_Mutationrs757010684A124T0.26
STADchr494587073Intronrs1816856320.14
STADchr494455332Missense_MutationnovelG15D0.3
STADchr494654544SilentNAI456I0.08
STADchr494618171In_Frame_InsnovelQ364dup0.14
STADchr494575829Missense_Mutationrs761636570V169I0.29
STADchr494587095Intronnovel0.36
STADchr494654613SilentNAC479C0.2
STADchr494585005Intronnovel0.19
STADchr494618054Missense_Mutationrs115018620R324Q0.3
STADchr494657440Missense_Mutationrs763438199A493V0.27
TGCTchr494575829Missense_MutationnovelV169L0.26
UCECchr494575748Missense_MutationnovelS142P0.05
UCECchr494575656Missense_MutationnovelS111Y0.34
UCECchr494584657Intronnovel0.5
UCECchr494662480SilentnovelG548G0.18
UCECchr494618164Missense_MutationnovelP361S0.53
UCECchr494523735Silentrs754256480G36G0.07
UCECchr494455349Missense_Mutationrs767631926G21S0.54
UCECchr4946664863'UTRnovel0.39
UCECchr494575641Missense_MutationnovelP106H0.37
UCECchr494585001Intronnovel0.53
UCECchr4946664453'UTRnovel0.26
UCECchr494662497Missense_MutationnovelA554D0.34
UCECchr494523768Silentrs757246202G47G0.44
UCECchr494575819Silentrs116148450P165P0.45
UCECchr494587095Intronnovel0.37
UCECchr494657479Missense_MutationnovelV506A0.06
UCECchr4946641553'UTRNA0.2
UCECchr494654528Missense_MutationnovelN451S0.22
UCECchr494640414Missense_MutationNAR416Q0.06
UCECchr494523772Missense_MutationNAV49M0.48
UCECchr494584795Intronnovel0.36
UCECchr494584644Intronnovel0.42
UCECchr494654617Nonsense_MutationnovelR481*0.32
UCECchr494584812Intronnovel0.08
UCECchr494575641Missense_MutationnovelP106H0.29
UCECchr494662530Missense_MutationnovelV565E0.24
UCECchr494575764Missense_Mutationrs147707993S147L0.31
UCECchr494610263Intronnovel0.36
UCECchr494575933SilentnovelV203V0.41
UCECchr494585002Intronrs3706699200.57
UCECchr494587091Intronnovel0.34
UCECchr494584672Intronnovel0.46
UCECchr494585573Missense_MutationnovelR240I0.38
UCECchr4946664563'UTRnovel0.46
UCECchr494575909Silentrs773177005S195S0.35
UCECchr494662510SilentnovelT558T0.08
UCECchr494587188Intronnovel0.4
UCECchr494610207Intronrs5358551050.39
UCECchr494584791Intronnovel0.32
UCECchr494586406Splice_Siters763032076X295_splice0.33
UCECchr494584752Intronnovel0.3
UCECchr4944552665'UTRnovel0.48
UCECchr494654617Nonsense_MutationnovelR481*0.17
UCECchr494575716Missense_MutationnovelP131H0.41
UCECchr494608123Intronnovel0.24
UCECchr494575628Nonsense_MutationnovelE102*0.07
UCECchr494654503Nonsense_MutationNAE443*0.27
UCECchr494575887Missense_MutationNAD188G0.44
UCECchr494584914Intronnovel0.24
UCECchr494587132Intronnovel0.22
UCECchr494585564Splice_SitenovelX237_splice0.32
UCECchr494662447Missense_Mutationrs115802510I537M0.08
UCECchr494657504SilentnovelN514N0.4
UCECchr494654598Missense_Mutationrs756291512F474L0.26
UCECchr494455246Splice_Sitenovel0.33
UCECchr494575713Missense_Mutationrs752588919R130Q0.54
UCECchr494576026Missense_MutationnovelQ234H0.49
UCECchr494657504SilentnovelN514N0.26
UCECchr494523817Missense_MutationNAL64I0.35

Copy Number Variations (CNVs)
CancerTypeFreq Q-value
LIHCDEL0.4277.0927e-07
LUADDEL0.19570.050802
MESODEL0.39080.075661

Survival Analysis
CancerP-value Q-value
THYM0.019

Kaplan-Meier Survival Analysis

KIRC0.0015

Kaplan-Meier Survival Analysis

STAD0.035

Kaplan-Meier Survival Analysis

SARC0.042

Kaplan-Meier Survival Analysis

SKCM0.0018

Kaplan-Meier Survival Analysis

KIRP0.023

Kaplan-Meier Survival Analysis

PAAD0.00073

Kaplan-Meier Survival Analysis

LAML0.011

Kaplan-Meier Survival Analysis

KICH0.029

Kaplan-Meier Survival Analysis

UCEC0.027

Kaplan-Meier Survival Analysis

GBM0.041

Kaplan-Meier Survival Analysis

LGG0.00011

Kaplan-Meier Survival Analysis

LUAD0.0079

Kaplan-Meier Survival Analysis

Drugs

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Eesembl ID



Cell lines and drugs in GSE70138 or GSE92742

  • Description
  • RBPome
  • Literatures
  • Expression
  • Transcripts
  • Gene Model
  • Phenotypes
  • GWAS
  • PPI
  • Orthologs
  • Gene Ontology
Description
Ensembl ID
ENSG00000163110 (Gene tree)
Gene ID
10611
Gene Symbol
PDLIM5
Alias
LIM|Enh
Full Name
PDZ and LIM domain 5
Gene Type
protein_coding
Species
Homo_sapiens
Status
confidence
Strand
Plus strand
Length
216,371 bases
Position
chr4:94,451,857-94,668,227
Accession
17468
RBP type
non-canonical RBP
Summary
This gene encodes a member of a family of proteins that possess a 100-amino acid PDZ domain at the N terminus and one to three LIM domains at the C-terminus. This family member functions as a scaffold protein that tethers protein kinases to the Z-disk in striated muscles. It is thought to function in cardiomyocyte expansion and in restraining postsynaptic growth of excitatory synapses. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]
RNA binding proteome (RBPome)
PIDTitleMethod TimeAuthorDoi
30607034Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)OOPS & HEK2932019 Jan 3Queiroz RMLDOI: 10.1038/s41587-018-0001-2
30528433The Human RNA-Binding Proteome and Its Dynamics during Translational ArrestXRNAX & HEK2932018 Dec 6Trendel JDOI: 10.1016/j.cell.2018.11.004
30528433The Human RNA-Binding Proteome and Its Dynamics during Translational ArrestXRNAX & Hela2018 Dec 6Trendel JDOI: 10.1016/j.cell.2018.11.004
30607034Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)OOPS & MCF10A2019 Jan 3Queiroz RMLDOI: 10.1038/s41587-018-0001-2
30607034Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)OOPS & U2OS2019 Jan 3Queiroz RMLDOI: 10.1038/s41587-018-0001-2
27453046Comprehensive Identification of RNA-Binding Domains in Human CellsRIC & Hela2016 Aug 18Castello ADOI: 10.1016/j.molcel.2016.06.029

Literatures on RNA binding capacity
PIDTitleArticle TimeAuthorDoi
27289039RBM20 and RBM24 cooperatively promote the expression of short enh splice variants.FEBS Lett2016 JulIto Jdoi: 10.1002/1873-3468.12251
Expression
Transcripts
Transcript IDNameLengthRefSeq ID Protein IDLengthRefSeq IDUniportKB ID
ENST00000511767PDLIM5-216463--- (aa)--
ENST00000359265PDLIM5-2031189-ENSP00000352210136 (aa)-Q96HC4
ENST00000380180PDLIM5-2052020-ENSP00000369527234 (aa)-Q96HC4
ENST00000508216PDLIM5-2101794XM_024453877ENSP00000426804234 (aa)XP_024309645Q96HC4
ENST00000318007PDLIM5-2021960-ENSP00000322021214 (aa)-Q96HC4
ENST00000542407PDLIM5-2212979XM_005262698ENSP00000442187487 (aa)XP_005262755Q96HC4
ENST00000627587PDLIM5-2231853-ENSP0000048693839 (aa)-A0A0D9SFW3
ENST00000504489PDLIM5-208538-ENSP0000042300938 (aa)-D6RAA1
ENST00000380176PDLIM5-2043098--- (aa)--
ENST00000509357PDLIM5-213554-ENSP0000042283385 (aa)-H0Y929
ENST00000509333PDLIM5-212743--- (aa)--
ENST00000514743PDLIM5-2193356-ENSP00000424360625 (aa)-Q96HC4
ENST00000508531PDLIM5-211480--- (aa)--
ENST00000506632PDLIM5-209907-ENSP00000422528231 (aa)-H0Y8Y3
ENST00000512274PDLIM5-217372-ENSP0000042637947 (aa)-D6RGG6
ENST00000437932PDLIM5-2065713-ENSP00000398469271 (aa)-A0A0A0MSP3
ENST00000514830PDLIM5-220802--- (aa)--
ENST00000510099PDLIM5-214554-ENSP00000486834176 (aa)-A0A0D9SFR4
ENST00000615540PDLIM5-2226219XM_005262693ENSP00000480359625 (aa)XP_005262750Q96HC4
ENST00000317968PDLIM5-2016083XM_006714069ENSP00000321746596 (aa)XP_006714132Q96HC4
ENST00000511586PDLIM5-215547--- (aa)--
ENST00000503974PDLIM5-2072081-ENSP00000424297483 (aa)-Q96HC4
ENST00000513341PDLIM5-218794-ENSP00000429577196 (aa)-H0YBI4
Gene Model
Click here to download ENSG00000163110's gene model file
Phenotypes
ensgIDTraitpValuePubmed ID
ENSG00000163110Cholesterol1.71584995678021E-617903299
ENSG00000163110Cholesterol2.03694257139506E-617903299
ENSG00000163110Cholesterol, LDL3.63075972197746E-717903299
ENSG00000163110Cholesterol, LDL5.44259226958239E-917903299
ENSG00000163110Parietal Lobe6.20174811485352E-517903297
ENSG00000163110Parietal Lobe3.09990700411156E-517903297
ENSG00000163110Parietal Lobe8.52998395484139E-517903297
ENSG00000163110Citalopram5.0800000E-005-
ENSG00000163110Citalopram9.2800000E-005-
ENSG00000163110Myocardial Infarction2.1840000E-005-
ENSG00000163110Myocardial Infarction1.8900000E-005-
ENSG00000163110Myocardial Infarction2.1090000E-005-
ENSG00000163110Myocardial Infarction1.8790000E-005-
ENSG00000163110Myocardial Infarction1.7660000E-005-
ENSG00000163110Myocardial Infarction1.2750000E-005-
ENSG00000163110Arterial Pressure6.5936251E-005-
ENSG00000163110Prostatic Neoplasms5E-622219177
ENSG00000163110Amyotrophic lateral sclerosis 16E-624529757
ENSG00000163110PCSK9 protein, human5E-625089948
ENSG00000163110Simvastatin5E-625089948
ENSG00000163110Pancreatitis3E-727114598
ENSG00000163110Precursor Cell Lymphoblastic Leukemia-Lymphoma3E-727114598
ENSG00000163110Electrocardiography6E-623166209
ENSG00000163110Adipose Tissue9E-622589738
ENSG00000163110Estradiol5E-723518928
ENSG00000163110Lewy Body Disease8E-625188341
ENSG00000163110Prostatic Neoplasms4E-1519767753
ENSG00000163110Prostatic Neoplasms1E-1119767753
GWAS
ensgIDSNPChromosomePositionSNP-risk TraitPubmedID95% CIOr or BEAT EFO ID
ENSG00000163110rs11731606494534108TMean platelet volume27863252[0.017-0.035] unit decrease0.0259829EFO_0004584
ENSG00000163110rs200495769494573377TAsparaginase-induced acute pancreatitis in acute lymphoblastic leukemia (onset time)271145985.7EFO_1001507|EFO_0000220
ENSG00000163110rs17021918494641726?Prostate cancer19767753[1.08-1.15]1.11EFO_0001663
ENSG00000163110rs12500426494593458?Prostate cancer19767753[1.05-1.12]1.08EFO_0001663
ENSG00000163110rs2452600494575731TCoronary artery disease29212778[0.023-0.05] unit decrease0.0365EFO_0000378
ENSG00000163110rs17336353494595365GResponse to simvastatin treatment (PCSK9 protein level change)25089948[NR] unit increase0.151GO_1903491|EFO_0006899
ENSG00000163110rs2452591494555568ALewy body disease25188341[0.15-0.39] unit decrease0.2693EFO_0006792|EFO_0006799
ENSG00000163110rs71581597494636417?Heel bone mineral density30048462[0.014-0.024] unit increase0.0188892EFO_0009270
ENSG00000163110rs12511169494652847TPulse pressure30578418[0.096-0.174] mmHg increase0.1351EFO_0005763
ENSG00000163110rs17021918494641726CProstate cancer29892016[1.07-1.11]1.09EFO_0001663
Protein-Protein Interaction (PPI)

Clik here to download ENSG00000163110's network

* RBP PPI network refers to all genes directly bind to RBP
Orthologs identified by RBPome
Ensembl IDGene SymbolCoverageIdentiy OrthologGene SymbolCoverageIdentiy Species
ENSG00000163110PDLIM59995.833ENSMUSG00000028273Pdlim510094.393Mus_musculus
Gene Ontology
Go IDGo_termPubmedIDEvidenceCategory
GO:0003779actin binding-ISSFunction
GO:0005080protein kinase C binding-ISSFunction
GO:0005515protein binding16549780.25416956.IPIFunction
GO:0005829cytosol-ISSComponent
GO:0005913cell-cell adherens junction25468996.HDAComponent
GO:0014069postsynaptic density-ISSComponent
GO:0015629actin cytoskeleton-IDAComponent
GO:0016020membrane-ISSComponent
GO:0042805actinin binding-ISSFunction
GO:0043005neuron projection-IEAComponent
GO:0045211postsynaptic membrane-IEAComponent
GO:0046872metal ion binding-IEAFunction
GO:0047485protein N-terminus binding-IEAFunction
GO:0051963regulation of synapse assembly-ISSProcess
GO:0061001regulation of dendritic spine morphogenesis-ISSProcess
GO:0061049cell growth involved in cardiac muscle cell development-ISSProcess
GO:0098609cell-cell adhesion-IEAProcess
GO:0098641cadherin binding involved in cell-cell adhesion25468996.HDAFunction
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