Browse LIMD1

Summary
SymbolLIMD1
NameLIM domains containing 1
Aliases LIM domain-containing protein 1
Chromosomal Location3p21.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Cytoplasm. Nucleus. Cytoplasm, P-body. Cell junction, adherens junction. Cell junction, focal adhesion. Note=Shuttles between cytoplasm and nucleus but is localized predominantly to the cytoplasm. Found in the nucleus but not nucleoli. Colocalizes with VCL in the focal adhesions. Down-regulation and/or elimination of its expression from the nucleus of neoplastic cells correlates strongly with poor patient prognosis and aggressive forms of breast carcinoma. Conversely, strong nuclear localization correlates with low-tumor grade and better patient prognosis.
Domain PF00412 LIM domain
Function

Adapter or scaffold protein which participates in the assembly of numerous protein complexes and is involved in several cellular processes such as cell fate determination, cytoskeletal organization, repression of gene transcription, cell-cell adhesion, cell differentiation, proliferation and migration. Positively regulates microRNA (miRNA)-mediated gene silencing and is essential for P-body formation and integrity. Acts as a hypoxic regulator by bridging an association between the prolyl hydroxylases and VHL enabling efficient degradation of HIF1A. Acts as a transcriptional corepressor for SNAI1- and SNAI2/SLUG-dependent repression of E-cadherin transcription. Negatively regulates the Hippo signaling pathway and antagonizes phosphorylation of YAP1. Inhibits E2F-mediated transcription, and suppresses the expression of the majority of genes with E2F1-responsive elements. Regulates osteoblast development, function, differentiation and stress osteoclastogenesis. Enhances the ability of TRAF6 to activate adapter protein complex 1 (AP-1) and negatively regulates the canonical Wnt receptor signaling pathway in osteoblasts. May act as a tumor suppressor by inhibiting cell proliferation.

> Gene Ontology
 
Biological Process GO:0001503 ossification
GO:0001649 osteoblast differentiation
GO:0001666 response to hypoxia
GO:0002076 osteoblast development
GO:0006417 regulation of translation
GO:0008360 regulation of cell shape
GO:0010608 posttranscriptional regulation of gene expression
GO:0016055 Wnt signaling pathway
GO:0016441 posttranscriptional gene silencing
GO:0016458 gene silencing
GO:0017148 negative regulation of translation
GO:0022604 regulation of cell morphogenesis
GO:0022613 ribonucleoprotein complex biogenesis
GO:0022618 ribonucleoprotein complex assembly
GO:0030111 regulation of Wnt signaling pathway
GO:0030178 negative regulation of Wnt signaling pathway
GO:0030278 regulation of ossification
GO:0030279 negative regulation of ossification
GO:0031047 gene silencing by RNA
GO:0033962 cytoplasmic mRNA processing body assembly
GO:0034248 regulation of cellular amide metabolic process
GO:0034249 negative regulation of cellular amide metabolic process
GO:0035194 posttranscriptional gene silencing by RNA
GO:0035195 gene silencing by miRNA
GO:0035329 hippo signaling
GO:0035330 regulation of hippo signaling
GO:0035331 negative regulation of hippo signaling
GO:0036293 response to decreased oxygen levels
GO:0040029 regulation of gene expression, epigenetic
GO:0045667 regulation of osteoblast differentiation
GO:0045668 negative regulation of osteoblast differentiation
GO:0060070 canonical Wnt signaling pathway
GO:0060147 regulation of posttranscriptional gene silencing
GO:0060148 positive regulation of posttranscriptional gene silencing
GO:0060828 regulation of canonical Wnt signaling pathway
GO:0060964 regulation of gene silencing by miRNA
GO:0060966 regulation of gene silencing by RNA
GO:0060968 regulation of gene silencing
GO:0070482 response to oxygen levels
GO:0071826 ribonucleoprotein complex subunit organization
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:0198738 cell-cell signaling by wnt
GO:1902532 negative regulation of intracellular signal transduction
GO:2000637 positive regulation of gene silencing by miRNA
Molecular Function GO:0003714 transcription corepressor activity
Cellular Component GO:0000932 cytoplasmic mRNA processing body
GO:0005667 transcription factor complex
GO:0005924 cell-substrate adherens junction
GO:0005925 focal adhesion
GO:0016442 RISC complex
GO:0030055 cell-substrate junction
GO:0031332 RNAi effector complex
GO:0035770 ribonucleoprotein granule
GO:0036464 cytoplasmic ribonucleoprotein granule
> KEGG and Reactome Pathway
 
KEGG hsa04390 Hippo signaling pathway
Reactome R-HSA-2262749: Cellular response to hypoxia
R-HSA-2262752: Cellular responses to stress
R-HSA-1234176: Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-HSA-1234174: Regulation of Hypoxia-inducible Factor (HIF) by oxygen
Summary
SymbolLIMD1
NameLIM domains containing 1
Aliases LIM domain-containing protein 1
Chromosomal Location3p21.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between LIMD1 and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 

There is no record.

Summary
SymbolLIMD1
NameLIM domains containing 1
Aliases LIM domain-containing protein 1
Chromosomal Location3p21.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of LIMD1 in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NS NA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NS NA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR Second most enriched score: 0.64 Sensitive to T cell-mediated killing
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NS NA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NS NA/NS
24476824shRNAmelanomaB16Primary screen NA/NS NA/NS
24476824shRNAmelanomaB16Secondary screen NA/NS NA/NS
Summary
SymbolLIMD1
NameLIM domains containing 1
Aliases LIM domain-containing protein 1
Chromosomal Location3p21.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of LIMD1 in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.6860.082
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.2190.865
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-1.3550.2
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160.3010.34
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590.4260.849
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.140.959
729033130MelanomaallAnti-PD-1 (nivolumab) 2623-0.0490.889
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.3360.826
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 1112-0.440.789
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.0870.922
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.6830.566
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.040.642
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of LIMD1 in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 277301.4-1.41
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 275901.7-1.71
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21174.804.81
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13117.707.71
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160001
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38270001
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22130001
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16140001
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 111307.7-7.71
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 51208.3-8.31
Summary
SymbolLIMD1
NameLIM domains containing 1
Aliases LIM domain-containing protein 1
Chromosomal Location3p21.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of LIMD1. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolLIMD1
NameLIM domains containing 1
Aliases LIM domain-containing protein 1
Chromosomal Location3p21.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of LIMD1. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by LIMD1.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolLIMD1
NameLIM domains containing 1
Aliases LIM domain-containing protein 1
Chromosomal Location3p21.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of LIMD1. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolLIMD1
NameLIM domains containing 1
Aliases LIM domain-containing protein 1
Chromosomal Location3p21.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of LIMD1 expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolLIMD1
NameLIM domains containing 1
Aliases LIM domain-containing protein 1
Chromosomal Location3p21.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between LIMD1 and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolLIMD1
NameLIM domains containing 1
Aliases LIM domain-containing protein 1
Chromosomal Location3p21.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting LIMD1 collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.