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ODC1
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IMMUNE CELL CELL LINEAGES Show tissue menu
B-CELLS DENDRITIC CELLS GRANULOCYTES MONOCYTES NK-CELLS PROGENITORS T-CELLS TOTAL PBMC
Immune cell proteome
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.

ODC1
Gene descriptioni

Full gene name according to HGNC.

Ornithine decarboxylase 1
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.

Intracellular
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.

Non-specific - Mitochondrial translation (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.

Low immune cell specificity
Tau specificity scorei

Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.

0.49
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.

Detected in many
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.

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.

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).

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.

Lineage
Expression
Alphabetical
Schmiedel dataseti

Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset.

Lineage
Expression
Alphabetical
EXPRESSION CLUSTERING & CORRELATIONi

The RNA data was used to cluster genes according to their expression across samples. The resulting clusters have been manually annotated to describe common features in terms of function and specificity. The annotation of the cluster is displayed together with a confidence score of the gene's assignment to the cluster. The confidence is calculated as the fraction of times the gene was assigned to this cluster in repeated calculations and is reported between 0 to 1, where 1 is the highest possible confidence. The clustering results are shown in a UMAP, where the cluster this gene was assigned to is highlighted as a colored area in which most of the cluster genes reside. A table shows the 15 most similar genes in terms of expression profile.

ODC1 is part of cluster 12 Non-specific - Mitochondrial translation with confidencei

Confidence is the fraction of times a gene was assigned to the cluster in repeated clustering, and therefore reflects how strongly associated it is to the cluster. A confidence of 1 indicates that the gene was assigned to this cluster in all repeated clusterings.

0.6
566 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.

Clusteri

ID of the expression cluster of the neighboring gene.

BLNK B cell linker 1.0000 12
TXNDC5 Thioredoxin domain containing 5 1.0000 12
MZB1 Marginal zone B and B1 cell specific protein 1.0000 12
SPIB Spi-B transcription factor 0.9762 12
RNASEH2B Ribonuclease H2 subunit B 0.9762 12
IGLJ5 Immunoglobulin lambda joining 5 (non-functional) 0.9762 23
SNTA1 Syntrophin alpha 1 0.9524 23
OIP5 Opa interacting protein 5 0.9524 12
BCL11A BAF chromatin remodeling complex subunit BCL11A 0.9524 12
SLC5A6 Solute carrier family 5 member 6 0.9524 13
TMEM19 Transmembrane protein 19 0.9524 23
CYB561A3 Cytochrome b561 family member A3 0.9524 12
TOR3A Torsin family 3 member A 0.9524 12
SCO2 Synthesis of cytochrome C oxidase 2 0.9286 12
SEC11C SEC11 homolog C, signal peptidase complex subunit 0.9286 12

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