Single cell type - MDK - 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.	MDK
Gene descriptionⁱ Full gene name according to HGNC.	Midkine
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes
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	Secreted
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	9

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	Fibroblasts - ECM organization (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	Cell type enhanced (Paneth cells, Enteroendocrine cells, Proximal enterocytes, Granulosa cells)
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	Immune cell enhanced (neutrophil, memory B-cell)
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 some
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	Cell line enhanced (NTERA-2, REH, SH-SY5Y)
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 many
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data. Read more	Protein predicted to be secreted

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: Cell type enhanced (Paneth cells, Enteroendocrine cells, Proximal enterocytes, Granulosa cells)

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

MDK is part of cluster 33 Fibroblasts - ECM organization with confidenceⁱ 1
171 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
BAMBI	BMP and activin membrane bound inhibitor	0.6271	40
MFAP2	Microfibril associated protein 2	0.6171	33
ALDH18A1	Aldehyde dehydrogenase 18 family member A1	0.5983	40
MAGED2	MAGE family member D2	0.5972	40
PLOD2	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2	0.5972	33
HSD17B2	Hydroxysteroid 17-beta dehydrogenase 2	0.5858	45
TMEM98	Transmembrane protein 98	0.5851	53
PIMREG	PICALM interacting mitotic regulator	0.5705	40
HAPLN1	Hyaluronan and proteoglycan link protein 1	0.5596	33
IHH	Indian hedgehog signaling molecule	0.5568	40
PRR15	Proline rich 15	0.5533	53
PRLR	Prolactin receptor	0.5487	36
P3H4	Prolyl 3-hydroxylase family member 4 (inactive)	0.5481	33
TMSB15A	Thymosin beta 15A	0.5476	40
GPX7	Glutathione peroxidase 7	0.5371	33

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	108.2 nTPM
Breast	117.4 nTPM
Adipose tissue	99.1 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	5.4 nTPM
Lung	5.4 nTPM

Astrocytes	5.5 nTPM
Brain	5.5 nTPM

B-cells	9.6 nTPM
Breast	56.2 nTPM
Colon	19.2 nTPM
Liver	6.6 nTPM
Stomach	5.9 nTPM
Bone marrow	4.1 nTPM
Lymph node	2.7 nTPM
Spleen	1.7 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM

Dendritic cells	5.4 nTPM
Breast	14.9 nTPM
Adipose tissue	1.3 nTPM
PBMC	0.0 nTPM

Endothelial cells	115.0 nTPM
Placenta	602.0 nTPM
Endometrium	174.3 nTPM
Breast	134.8 nTPM
Pancreas	112.0 nTPM
Esophagus	100.8 nTPM
Skin	87.4 nTPM
Skeletal muscle	79.8 nTPM
Prostate	68.5 nTPM
Ovary	57.7 nTPM
Liver	54.1 nTPM
Testis	48.9 nTPM
Eye	34.8 nTPM
Lung	31.2 nTPM
Heart muscle	23.8 nTPM

Enteroendocrine cells	1010.4 nTPM
Rectum	1203.7 nTPM
Colon	817.1 nTPM

Fibroblasts	275.2 nTPM
Placenta	1527.5 nTPM
Ovary	570.7 nTPM
Breast	341.6 nTPM
Stomach	103.9 nTPM
Prostate	103.8 nTPM
Esophagus	101.1 nTPM
Lung	99.4 nTPM
Skin	82.1 nTPM
Adipose tissue	40.0 nTPM
Heart muscle	32.4 nTPM
Skeletal muscle	24.1 nTPM

Intestinal goblet cells	368.8 nTPM
Small intestine	573.0 nTPM
Colon	318.0 nTPM
Rectum	215.3 nTPM

Macrophages	10.0 nTPM
Endometrium	55.3 nTPM
Ovary	28.2 nTPM
Prostate	19.5 nTPM
Breast	10.7 nTPM
Lung	8.8 nTPM
Kidney	6.1 nTPM
Pancreas	5.1 nTPM
Esophagus	4.8 nTPM
Skeletal muscle	3.2 nTPM
Spleen	3.1 nTPM
Testis	2.9 nTPM
Bone marrow	1.2 nTPM
Adipose tissue	1.1 nTPM
PBMC	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	1272.7 nTPM
Small intestine	1918.5 nTPM
Colon	1403.1 nTPM
Rectum	496.5 nTPM

Plasma cells	18.6 nTPM
Stomach	50.8 nTPM
Adipose tissue	18.8 nTPM
Esophagus	18.4 nTPM
Spleen	3.5 nTPM
Bone marrow	1.7 nTPM

Respiratory ciliated cells	109.5 nTPM
Bronchus	173.8 nTPM
Lung	45.2 nTPM

Smooth muscle cells	197.0 nTPM
Ovary	1191.4 nTPM
Bronchus	213.9 nTPM
Endometrium	186.5 nTPM
Adipose tissue	126.3 nTPM
Pancreas	123.6 nTPM
Esophagus	71.3 nTPM
Prostate	63.5 nTPM
Breast	62.2 nTPM
Skin	53.7 nTPM
Skeletal muscle	40.2 nTPM
Heart muscle	34.1 nTPM

Basal keratinocytes	11.1 nTPM
Skin	11.1 nTPM

Basal prostatic cells	162.1 nTPM
Prostate	162.1 nTPM

Basal respiratory cells	392.4 nTPM
Bronchus	392.4 nTPM

Basal squamous epithelial cells	12.5 nTPM
Esophagus	12.5 nTPM

T-cells	11.4 nTPM
Endometrium	91.5 nTPM
Prostate	28.4 nTPM
Colon	17.6 nTPM
Breast	16.3 nTPM
Skin	13.3 nTPM
Esophagus	6.6 nTPM
Ovary	4.5 nTPM
Skeletal muscle	3.5 nTPM
Kidney	3.4 nTPM
Lymph node	2.5 nTPM
Liver	2.1 nTPM
Lung	1.5 nTPM
Stomach	1.3 nTPM
PBMC	1.2 nTPM
Adipose tissue	0.5 nTPM
Bone marrow	0.4 nTPM
Spleen	0.0 nTPM

Undifferentiated cells	187.6 nTPM
Small intestine	350.5 nTPM
Rectum	110.5 nTPM
Colon	101.8 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