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
20714146PINCH protein expression in normal endometrium, atypical endometrial hyperplasia and endometrioid endometrial carcinoma.Chemotherapy2010Zhang HZdoi: 10.1159/000319953
18957717PINCH expression and its significance in esophageal squamous cell carcinoma.Dis Markers2008Zhu Z-
23970013PINCH expression in relation to radiation response in co-cultured colon cancer cells and in rectal cancer patients.Oncol Rep2013 NovHolmqvist Adoi: 10.3892/or.2013.2673
25647720Ras suppressor-1 promotes apoptosis in breast cancer cells by inhibiting PINCH-1 and activating p53-upregulated-modulator of apoptosis (PUMA); verification from metastatic breast cancer human samples.Clin Exp Metastasis2015 MarGiotopoulou Ndoi: 10.1007/s10585-015-9701-x
29079319Knockdown of PINCH-1 protein sensitizes the estrogen positive breast cancer cells to chemotherapy induced apoptosis.Pathol Res Pract2018 FebBhatia Adoi: 10.1016/j.prp.2017.09.026

Differential Expression

Expression in 33 cancers

Mutations
CancerChrPosition Mutation TypedbSNPProtein-change Allele FreqRBD
BLCAchr21086840943'UTRnovel0.56
BLCAchr2108655171Intronnovel0.26
BLCAchr2108675990Missense_MutationNAR203G0.63
BLCAchr2108683981SilentnovelE320E0.08
BLCAchr21086840283'UTRnovel0.21
BLCAchr2108672445Frame_Shift_InsnovelH116Tfs*80.14
BLCAchr2108678009Missense_Mutationrs770508766R257C0.66
BLCAchr2108683989Missense_Mutationrs748854260G323E0.14
BRCAchr2108683962Missense_MutationNAR314I0.22
BRCAchr2108659716Silentrs144584482F36F0.34
BRCAchr2108659677Silentrs375236817I23I0.18
BRCAchr2108672388Missense_MutationnovelR96L0.31
CESCchr2108676805Intronnovel0.49
CESCchr2108621421Intronrs1491190380.25
CESCchr2108675953SilentnovelV190V0.42
CESCchr2108676603Splice_Regionnovel0.14
CESCchr2108659669Missense_MutationNAE21K0.11
COADchr2108659666Missense_Mutationrs142167178A20T0.26
COADchr21086840543'UTRnovel0.32
COADchr21086841293'UTRnovel0.22
COADchr21086842383'Flanknovel0.12
COADchr2108607235Intronnovel0.24
COADchr21086840153'UTRnovel0.1
COADchr2108655029Intronnovel0.32
COADchr2108676648Missense_MutationNAR230C0.31
COADchr2108676666Nonsense_MutationnovelG236delinsV*DS0.04
COADchr2108680723SilentNAC272C0.08
COADchr2108659642Missense_Mutationrs200004487R12C0.19
DLBCchr2108659630Missense_Mutationrs375431434A8T0.1
ESCAchr2108672414Missense_MutationnovelA105T0.41
ESCAchr2108655006Intronnovel0.23
GBMchr2108675992Silentrs111779374R203R0.59
HNSCchr2108659747Missense_Mutationrs768178569E47K0.2
KIRCchr2108680708Frame_Shift_InsnovelN268Kfs*20.2
KIRPchr2108675983Silentrs758889895I200I0.44
KIRPchr21086840583'UTRnovel0.41
LGGchr2108659642Missense_Mutationrs200004487R12C0.27
LUADchr2108675992Silentrs111779374R203R0.16
LUSCchr2108659750Missense_Mutationrs773956158G48R0.17
LUSCchr2108659751Missense_Mutationrs761280581G48E0.17
LUSCchr2108655104Intronnovel0.3
LUSCchr2108659758SilentNAF50F0.14
OVchr2108659668SilentnovelA20A0.12
OVchr2108659669Nonsense_MutationnovelE21*0.12
PRADchr2108675992Silentrs111779374R203R0.4
READchr2108654913Intronnovel0.36
READchr21086840203'UTRnovel0.36
SKCMchr2108655042Intronrs7589120540.34
SKCMchr2108673012SilentnovelF159F0.31
SKCMchr2108683943Missense_MutationnovelP308S0.37
STADchr2108659698SilentnovelL30L0.1
STADchr2108678017Missense_MutationnovelI259M0.42
STADchr2108675895Missense_MutationNAD171G0.08
STADchr2108659660Missense_MutationnovelA18S0.09
THCAchr2108675943Missense_Mutationrs767129546K187R0.07
UCECchr2108675877Splice_SitenovelX165_splice0.3
UCECchr2108678028Splice_SiteNAX263_splice0.4
UCECchr2108670820Missense_MutationnovelL66F0.18
UCECchr2108672367Missense_MutationnovelS89I0.19
UCECchr2108680723SilentNAC272C0.33
UCECchr2108659716Silentrs144584482F36F0.27
UCECchr2108655009Intronnovel0.32
UCECchr2108675991Missense_Mutationrs377342624R203H0.37
UCECchr2108676649Missense_MutationNAR230H0.77
UCECchr2108672905Missense_MutationnovelR124C0.63
UCECchr2108673027Splice_Regionrs779262048C164C0.62
UCECchr2108683965Missense_MutationnovelL315R0.36
UCECchr2108655094Intronnovel0.53
UCECchr2108659640Missense_MutationNAE11G0.23
UCECchr2108672905Missense_MutationnovelR124C0.38
UCECchr2108670798Nonsense_MutationnovelY58*0.49
UCECchr2108621294Intronnovel0.38
UCECchr2108655127IntronNA0.38
UCECchr2108675901Missense_MutationnovelR173L0.34
UCECchr21086840273'UTRrs7785191320.45
UCECchr2108659716Silentrs144584482F36F0.07
UCECchr2108672967Missense_MutationNAE144D0.27
UVMchr2108680747SilentnovelT280T0.34

Copy Number Variations (CNVs)
CancerTypeFreq Q-value
ACCDEL0.17780.15279
PAADDEL0.03260.2014

Survival Analysis
CancerP-value Q-value
THYM0.014

Kaplan-Meier Survival Analysis

UCS0.0096

Kaplan-Meier Survival Analysis

HNSC0.025

Kaplan-Meier Survival Analysis

SKCM0.001

Kaplan-Meier Survival Analysis

TGCT0.047

Kaplan-Meier Survival Analysis

KIRP0.00028

Kaplan-Meier Survival Analysis

PAAD0.011

Kaplan-Meier Survival Analysis

CESC0.032

Kaplan-Meier Survival Analysis

LAML0.012

Kaplan-Meier Survival Analysis

KICH0.033

Kaplan-Meier Survival Analysis

UCEC0.037

Kaplan-Meier Survival Analysis

LIHC0.0027

Kaplan-Meier Survival Analysis

LGG0.0001

Kaplan-Meier Survival Analysis

THCA0.04

Kaplan-Meier Survival Analysis

OV0.035

Kaplan-Meier Survival Analysis

Drugs

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Eesembl ID



Cell lines and drugs in GSE70138 or GSE92742

  • Description
  • RBPome
  • Expression
  • Transcripts
  • Gene Model
  • GWAS
  • PPI
  • Gene Ontology
Description
Ensembl ID
ENSG00000169756 (Gene tree)
Gene ID
3987
Gene Symbol
LIMS1
Alias
PINCH|PINCH1
Full Name
LIM zinc finger domain containing 1
Gene Type
protein_coding
Species
Homo_sapiens
Status
putative
Strand
Plus strand
Length
152,892 bases
Position
chr2:108,534,355-108,687,246
Accession
6616
RBP type
non-canonical RBP
Summary
The protein encoded by this gene is an adaptor protein which contains five LIM domains, or double zinc fingers. The protein is likely involved in integrin signaling through its LIM domain-mediated interaction with integrin-linked kinase, found in focal adhesion plaques. It is also thought to act as a bridge linking integrin-linked kinase to NCK adaptor protein 2, which is involved in growth factor receptor kinase signaling pathways. Its localization to the periphery of spreading cells also suggests that this protein may play a role in integrin-mediated cell adhesion or spreading. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
RNA binding proteome (RBPome)
PIDTitleMethod TimeAuthorDoi
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
Expression
Transcripts
Transcript IDNameLengthRefSeq ID Protein IDLengthRefSeq IDUniportKB ID
ENST00000422797LIMS1-2071544-ENSP00000402322100 (aa)-F8WE10
ENST00000338045LIMS1-2021876XM_005263946ENSP00000337598387 (aa)XP_005264003P48059
ENST00000449684LIMS1-210492--- (aa)--
ENST00000462817LIMS1-211566--- (aa)--
ENST00000434274LIMS1-209779-ENSP0000041075155 (aa)-F8WB59
ENST00000393310LIMS1-2034392XM_005263951ENSP00000376987325 (aa)XP_005264008P48059
ENST00000414829LIMS1-206439XM_017004096ENSP00000399267117 (aa)XP_016859585F8WC86
ENST00000410093LIMS1-2051526-ENSP00000386926329 (aa)-P48059
ENST00000332345LIMS1-2011235XM_005263950ENSP00000331775325 (aa)XP_005264007P48059
ENST00000428064LIMS1-208637-ENSP00000390862176 (aa)-C9JF46
ENST00000409441LIMS1-2041627XM_005263948ENSP00000387264362 (aa)XP_005264005P48059
ENST00000474038LIMS1-212679--- (aa)--
ENST00000542845LIMS1-214727-ENSP00000446121209 (aa)-A0A0M3HER1
ENST00000544547LIMS1-2154461XM_005263949ENSP00000437912337 (aa)XP_005264006P48059
ENST00000496653LIMS1-213626--- (aa)--
Gene Model
Click here to download ENSG00000169756's gene model file
GWAS
ensgIDSNPChromosomePositionSNP-risk TraitPubmedID95% CIOr or BEAT EFO ID
ENSG00000169756rs65427722108558159CExcessive hairiness29895819[1.17-1.37]1.27HP_0001007
ENSG00000169756rs1119959662108558513GMonocyte chemoattractant protein-1 levels27989323[0.084-0.206] SD units decrease0.1452EFO_0004749
ENSG00000169756rs18661882108640696AEyebrow thickness30248107EFO_0007823
ENSG00000169756rs8266812108615619C Low density lipoprotein cholesterol levels29507422unit decrease0.025EFO_0004611
ENSG00000169756rs8266812108615619C Total cholesterol levels29507422unit decrease0.025EFO_0004574
Protein-Protein Interaction (PPI)

Clik here to download ENSG00000169756's network

* RBP PPI network refers to all genes directly bind to RBP
Gene Ontology
Go IDGo_termPubmedIDEvidenceCategory
GO:0001837epithelial to mesenchymal transition20926685.IMPProcess
GO:0005515protein binding10574708.12432066.15721255.18339839.19074270.20926685.21390327.23088713.23414517.23455922.23877428.25416956.25852190.IPIFunction
GO:0005829cytosol-TASComponent
GO:0005886plasma membrane-IEAComponent
GO:0005911cell-cell junction20926685.IMPComponent
GO:0005925focal adhesion21423176.HDAComponent
GO:0005925focal adhesion20926685.21390327.IDAComponent
GO:0005925focal adhesion19117955.IDAComponent
GO:0007569cell aging7517666.TASProcess
GO:0008270zinc ion binding19074270.IDAFunction
GO:0010628positive regulation of gene expression20926685.IMPProcess
GO:0010811positive regulation of cell-substrate adhesion20926685.IMPProcess
GO:0019901protein kinase binding20926685.IPIFunction
GO:0032991protein-containing complex-IEAComponent
GO:0033209tumor necrosis factor-mediated signaling pathway21343177.IMPProcess
GO:0034329cell junction assembly-TASProcess
GO:0043547positive regulation of GTPase activity20926685.IMPProcess
GO:0045184establishment of protein localization20926685.IMPProcess
GO:0045892negative regulation of transcription, DNA-templated21390327.IDAProcess
GO:0048471perinuclear region of cytoplasm21390327.IDAComponent
GO:0050678regulation of epithelial cell proliferation20926685.IMPProcess
GO:0051291protein heterooligomerization-IEAProcess
GO:0051894positive regulation of focal adhesion assembly20926685.IMPProcess
GO:0071560cellular response to transforming growth factor beta stimulus21390327.IEPProcess
GO:1900026positive regulation of substrate adhesion-dependent cell spreading20926685.IMPProcess
GO:1901224positive regulation of NIK/NF-kappaB signaling21343177.IMPProcess
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