Single cell type - PHYKPL - The Human Protein Atlas

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.	PHYKPL
Gene descriptionⁱ Full gene name according to HGNC.	5-phosphohydroxy-L-lysine phospho-lyase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Metabolic proteins Potential drug targets
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
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	3

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Single cell type expression clusterⁱ 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	Non-specific - Transcription (mainly)
Single cell type specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell types based on scRNA-seq data from normal tissues. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. Read more	Low cell type specificity
Immune cell 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 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
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Low cell line specificity
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in all
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of single cell RNA (nTPM) from all single cell types. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.
Single cell types Group Expression Alphabetical RNA single cell type specificity: Low cell type specificity

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

PHYKPL is part of cluster 52 Non-specific - Transcription with confidenceⁱ 1
611 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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
IRF9	Interferon regulatory factor 9	0.5109	52
POLM	DNA polymerase mu	0.5066	52
PARP10	Poly(ADP-ribose) polymerase family member 10	0.5006	63
SLC25A45	Solute carrier family 25 member 45	0.4977	63
PRR13	Proline rich 13	0.4855	45
N4BP2L2	NEDD4 binding protein 2 like 2	0.4850	52
AOC1	Amine oxidase copper containing 1	0.4715	45
C19orf25	Chromosome 19 open reading frame 25	0.4691	52
SH3BP1	SH3 domain binding protein 1	0.4689	63
PLAC8	Placenta associated 8	0.4684	53
GLI4	GLI family zinc finger 4	0.4641	39
TTC24	Tetratricopeptide repeat domain 24	0.4636	59
TDP2	Tyrosyl-DNA phosphodiesterase 2	0.4547	45
IL2RG	Interleukin 2 receptor subunit gamma	0.4494	58
TRIM73	Tripartite motif containing 73	0.4464	40

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	23.1 nTPM
Breast	24.4 nTPM
Adipose tissue	21.8 nTPM

Alveolar cells type 1	19.2 nTPM
Lung	19.2 nTPM

Alveolar cells type 2	14.3 nTPM
Lung	14.3 nTPM

Astrocytes	31.6 nTPM
Brain	31.6 nTPM

B-cells	63.0 nTPM
PBMC	85.6 nTPM
Stomach	83.1 nTPM
Spleen	76.1 nTPM
Bone marrow	76.0 nTPM
Colon	75.1 nTPM
Lymph node	66.2 nTPM
Kidney	47.6 nTPM
Adipose tissue	44.6 nTPM
Liver	39.2 nTPM
Breast	36.0 nTPM

Dendritic cells	72.5 nTPM
PBMC	131.5 nTPM
Breast	45.6 nTPM
Adipose tissue	40.3 nTPM

Endothelial cells	26.2 nTPM
Prostate	38.0 nTPM
Esophagus	37.1 nTPM
Liver	35.7 nTPM
Testis	35.3 nTPM
Ovary	32.4 nTPM
Skeletal muscle	30.6 nTPM
Heart muscle	30.2 nTPM
Placenta	25.6 nTPM
Skin	22.3 nTPM
Breast	21.8 nTPM
Endometrium	21.2 nTPM
Eye	20.3 nTPM
Lung	9.3 nTPM
Pancreas	7.7 nTPM

Fibroblasts	33.4 nTPM
Adipose tissue	53.5 nTPM
Skeletal muscle	45.8 nTPM
Esophagus	44.2 nTPM
Stomach	41.6 nTPM
Breast	36.1 nTPM
Prostate	35.4 nTPM
Skin	29.4 nTPM
Placenta	25.0 nTPM
Ovary	21.1 nTPM
Lung	20.1 nTPM
Heart muscle	15.1 nTPM

Intestinal goblet cells	40.8 nTPM
Small intestine	47.0 nTPM
Colon	42.2 nTPM
Rectum	33.2 nTPM

Macrophages	43.3 nTPM
Stomach	70.3 nTPM
Bone marrow	62.5 nTPM
Kidney	58.2 nTPM
Prostate	53.9 nTPM
Ovary	50.0 nTPM
Testis	48.3 nTPM
Breast	45.3 nTPM
Adipose tissue	44.0 nTPM
Spleen	42.5 nTPM
Skeletal muscle	37.5 nTPM
Esophagus	36.2 nTPM
Pancreas	33.2 nTPM
PBMC	27.3 nTPM
Endometrium	23.9 nTPM
Lung	16.3 nTPM

Paneth cells	64.5 nTPM
Colon	95.5 nTPM
Rectum	60.4 nTPM
Small intestine	37.6 nTPM

Plasma cells	51.4 nTPM
Stomach	81.1 nTPM
Bone marrow	57.7 nTPM
Spleen	48.4 nTPM
Adipose tissue	45.2 nTPM
Esophagus	24.6 nTPM

Respiratory ciliated cells	13.6 nTPM
Bronchus	14.0 nTPM
Lung	13.1 nTPM

Smooth muscle cells	23.6 nTPM
Esophagus	48.0 nTPM
Skeletal muscle	39.2 nTPM
Ovary	26.1 nTPM
Breast	23.6 nTPM
Prostate	23.1 nTPM
Endometrium	20.3 nTPM
Adipose tissue	20.3 nTPM
Heart muscle	19.1 nTPM
Skin	16.7 nTPM
Pancreas	14.6 nTPM
Bronchus	8.4 nTPM

T-cells	58.9 nTPM
Stomach	119.6 nTPM
Colon	94.1 nTPM
PBMC	81.1 nTPM
Kidney	80.7 nTPM
Bone marrow	77.3 nTPM
Lymph node	72.2 nTPM
Spleen	63.3 nTPM
Liver	59.3 nTPM
Ovary	57.8 nTPM
Breast	50.5 nTPM
Endometrium	48.1 nTPM
Skeletal muscle	45.5 nTPM
Adipose tissue	42.1 nTPM
Esophagus	39.3 nTPM
Prostate	28.4 nTPM
Skin	27.6 nTPM
Lung	13.6 nTPM

Basal keratinocytes	10.7 nTPM
Skin	10.7 nTPM

Basal prostatic cells	43.1 nTPM
Prostate	43.1 nTPM

Basal respiratory cells	16.1 nTPM
Bronchus	16.1 nTPM

Cytotrophoblasts	18.4 nTPM
Placenta	18.4 nTPM

Undifferentiated cells	39.2 nTPM
Colon	41.9 nTPM
Small intestine	39.6 nTPM
Rectum	36.1 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC