Immune cell - LYSMD3 - The Human Protein Atlas

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LYSMD3

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TISSUE

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GENERAL INFORMATIONⁱ General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.
Gene nameⁱ Official gene symbol, which is typically a short form of the gene name, according to HGNC.	LYSMD3
Gene descriptionⁱ Full gene name according to HGNC.	LysM domain containing 3
Predicted locationⁱ All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions. Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached. Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s). The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location. Read more	Intracellular,Membrane

IMMUNE CELL SECTION SUMMARY
Immune cell type expression clusterⁱ The RNA data is used to cluster genes according to their expression across immune cells. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Basophils - Unknown function (mainly)
Immune cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low immune cell specificity
Immune cell type distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Detected in all
Immune cell lineage specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: lineage enriched, group enriched, lineage enhanced, low lineage specificity and not detected. Lineages include B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells. Read more	Low lineage specificity
Immune cell lineage distributionⁱ The RNA data was used to cluster genes according to their expression across single cell types. Clusters contain genes that have similar expression patterns, and each cluster has been manually annotated to describe common features in terms of function and specificity. Read more	Detected in all

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Read more Lineage Expression Alphabetical Immune cell type specificity: Low immune cell specificity
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Read more Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Read more Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

LYSMD3 is part of cluster 38 Basophils - Unknown function with confidenceⁱ 0.66
306 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on immune cell RNA expression

Neighbourⁱ Gene name according to HGNC.	Descriptionⁱ Gene description according to HGNC.	Correlationⁱ Correlation between the selected gene and neighboring gene. Correlation is calculated as Spearman correlation in PCA space based on the RNA-seq expression data. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
KLF5	Kruppel like factor 5	0.8136	38
PTGER3	Prostaglandin E receptor 3	0.8038	38
HTR1B	5-hydroxytryptamine receptor 1B	0.7846	38
ENPP3	Ectonucleotide pyrophosphatase/phosphodiesterase 3	0.7771	38
KRT18	Keratin 18	0.7740	38
TEX101	Testis expressed 101	0.7677	38
HOXA6	Homeobox A6	0.7584	38
ZC3H11A	Zinc finger CCCH-type containing 11A	0.7486	38
CA2	Carbonic anhydrase 2	0.7473	38
DENR	Density regulated re-initiation and release factor	0.7464	38
FCHO2	FCH and mu domain containing endocytic adaptor 2	0.7326	38
RPS6KC1	Ribosomal protein S6 kinase C1	0.7281	18
TUBA1C	Tubulin alpha 1c	0.7273	38
PAQR5	Progestin and adipoQ receptor family member 5	0.7086	38
EFCAB11	EF-hand calcium binding domain 11	0.7086	18

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.