Gene: LIM2

LinkedOmicsKB © 2022-2023 Zhang Lab

Basic information

Full name
lens intrinsic membrane protein 2
Ensembl
ENSG00000105370.8
Summary
This gene encodes an eye lens-specific protein found at the junctions of lens fiber cells, where it may contribute to cell junctional organization. It acts as a receptor for calmodulin, and may play an important role in both lens development and cataractogenesis. Mutations in this gene have been associated with cataract formation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

Protein product

  • ENST00000596399.2 Primary ENSP00000472090.2 (0 phosphosite)
  • ENST00000221973.7
Phosphosites on the primary protein product

Tumor and normal comparison

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Signed p-values
Data type
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
RNA-4.3e-4-1.1e-5--0.032-5.1e-8-6.6e-18--0.72-
protein-----------

* P-values are from Wilcoxon rank sum test and can be clicked to show the box plots. Positive values mean higher abundance in tumor. BRCA and GBM do not have normal samples.

mRNA expression at gene level
BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC012345678log2(RSEM+1)tumornormal
Protein expression

* Mild outlier: filled circle; Extreme outlier: empty circle.

Phenotype and mutation association

Manhattan plot summarizing associations of phenotypes and mutations across all cohorts and omics data types

BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC01234567890-1-2-3-4-5-6-7-8-9Pan-cancer0.00.51.01.52.02.53.03.54.04.55.05.56.00.0-0.5-1.0-1.5-2.0-2.5-3.0-3.5-4.0-4.5-5.0-5.5-6.0proteinRNASCNVclinicalpathwaycell typegenomicmutation-log10 of P-value

* Data points of significant associations above and below the dotted lines can be hovered to show the phenotype.

Associations of the protein abundance of LIM2 with phenotypes and mutations

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Signed p-values
Phenotype
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
cibersort: B cell naive-----------
cibersort: B cell memory-----------
cibersort: B cell plasma-----------
cibersort: T cell CD8+-----------
cibersort: T cell CD4+ naive-----------
cibersort: T cell CD4+ memory resting-----------
cibersort: T cell CD4+ memory activated-----------
cibersort: T cell follicular helper-----------
cibersort: T cell regulatory (Tregs)-----------
cibersort: T cell gamma delta-----------
Showing 1 to 10 of 256 rows

* P-values could be from test for Spearman correlation, Wilcoxon rank sum test, Jonckheere-Terpstra trend test or Cox regression depending on the data type. P-values for individual cohorts can be clicked to show the data plots. The matrix icons in each row can be clicked to show a heatmap summary of associations across all cohorts and omics. The rows in the table can be expanded to show results from other omics.

Cis-association

Associations between omics data of LIM2

BRCA-0.25proteinmRNASCNVmethylationCCRCC-0.05proteinmRNASCNVmethylationCOAD0.02proteinmRNASCNVmethylationGBM0.01proteinmRNASCNVmethylationHNSCC0.03proteinmRNASCNVmethylationLSCC0.01proteinmRNASCNVmethylationLUAD-0.06proteinmRNASCNVmethylationOV0.01proteinmRNASCNVmethylationPDAC0.08proteinmRNASCNVmethylationUCEC0.06proteinmRNASCNVmethylation

* The numbers are Spearman correlation coefficients and can be clicked to show the scatter plots. The color and size of the circles correlate with the coefficients.

Trans-association

Associations of the protein abundance of LIM2 and the protein abundance of other genes

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Signed p-values
Gene
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
No matching records found

* P-values are from test for Spearman correlation. P-values for individual cohorts can be clicked to show the data plots. The matrix icons in each row can be clicked to show a heatmap summary of associations across all cohorts and omics. The rows in the table can be expanded to show results from other omics.

Gene set enrichment analysis

Submit genes and the common logarithm of the p-values of their association with to WebGestalt.