Gene: CD4

LinkedOmicsKB © 2022-2023 Zhang Lab

Basic information

Full name
CD4 molecule
Ensembl
ENSG00000010610.10
Summary
This gene encodes the CD4 membrane glycoprotein of T lymphocytes. The CD4 antigen acts as a coreceptor with the T-cell receptor on the T lymphocyte to recognize antigens displayed by an antigen presenting cell in the context of class II MHC molecules. The CD4 antigen is also a primary receptor for entry of the human immunodeficiency virus through interactions with the HIV Env gp120 subunit. This gene is expressed not only in T lymphocytes, but also in B cells, macrophages, granulocytes, as well as in various regions of the brain. The protein functions to initiate or augment the early phase of T-cell activation, and may function as an important mediator of indirect neuronal damage in infectious and immune-mediated diseases of the central nervous system. Multiple alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, May 2020]
Annotation
Druggable target (Tier T2) Receptor

Protein product

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
RNA0.044-4.8e-28--1.2e-3-3.7e-17-5.7e-8--0.017-
protein0.09-6.8e-27-3.5e-3-3.5e-3-9.1e-40.78-0.290.091-0.31

* 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
BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC6.577.588.599.51010.51111.51212.513log2(RSEM+1)tumornormal
Protein expression
BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC1919.52020.52121.52222.52323.52424.525log2(MS1 intensity)tumornormal

* 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

BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC0510152025303540450-5-10-15-20-25-30-35-40-45Pan-cancer0204060801001201401601802002202402600-20-40-60-80-100-120-140-160-180-200-220-240-260proteinRNASCNVclinicalpathwaycell 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 CD4 with phenotypes and mutations

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Signed p-values
Phenotype
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
ESTIMATE: ImmuneScore1.0e-1262.2e-162.2e-164.2e-52.2e-162.2e-162.2e-162.2e-162.2e-162.2e-162.7e-9
HALLMARK_ALLOGRAFT_REJECTION1.5e-1202.2e-162.2e-161.4e-52.2e-162.2e-162.2e-162.2e-162.2e-161.1e-93e-9
ESTIMATE: ESTIMATEScore2.4e-1059.4e-102.2e-161.2e-42.2e-162.2e-162.2e-162.2e-162.2e-163.7e-82.5e-5
xcell: immune score1.9e-1042.2e-162.2e-168.7e-52.2e-162.2e-162.2e-162.2e-161.8e-71e-78.8e-7
xcell: microenvironment score1.7e-982.2e-162.2e-161.3e-42.2e-162.2e-162.2e-162.2e-163e-92.1e-64.4e-3
HALLMARK_IL6_JAK_STAT3_SIGNALING1.5e-972.2e-162.2e-160.0012.2e-162.2e-162.2e-162e-83.6e-105.5e-74.3e-7
HALLMARK_IL2_STAT5_SIGNALING7.7e-912.2e-161.3e-82.3e-42.2e-162.2e-162.2e-161.2e-82.2e-161.1e-56.7e-4
xcell: Macrophage5.7e-891.1e-82.2e-161.8e-52.2e-161.4e-145.3e-227.8e-71.1e-52.1e-53.6e-9
HALLMARK_COMPLEMENT1.3e-872.2e-162.2e-161.6e-32.2e-167.3e-152.2e-163.0e-56.8e-89.1e-77.2e-6
xcell: Macrophage M11.4e-843.3e-92.8e-156.6e-62.2e-169e-162.2e-163.1e-59e-72.2e-41.3e-9
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* 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 CD4

BRCA0.670.01-0.02proteinmRNASCNVmethylationCCRCC0.78-0.030.01proteinmRNASCNVmethylationCOAD0.40-0.07-0.01proteinmRNASCNVmethylationGBM0.880.180.09proteinmRNASCNVmethylationHNSCC0.86-0.08-0.07proteinmRNASCNVmethylationLSCC0.87-0.14-0.12proteinmRNASCNVmethylationLUAD0.72-0.07-0.17proteinmRNASCNVmethylationOV0.630.03-0.03proteinmRNASCNVmethylationPDAC0.440.130.12proteinmRNASCNVmethylationUCEC0.57-0.00-0.11proteinmRNASCNVmethylation

* 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 CD4 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.