Single cell type - PI3 - 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.	PI3
Gene descriptionⁱ Full gene name according to HGNC.	Peptidase inhibitor 3
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma proteins
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.	1

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	Respiratory epithelial cells - Mucosal defense (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	Group enriched (Basal respiratory cells, Club 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 enriched (neutrophil)
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	Group enriched (EFO-21, HaCaT, OE19, PC-3)
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: Group enriched (Basal respiratory cells, Club 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

PI3 is part of cluster 26 Respiratory epithelial cells - Mucosal defense with confidenceⁱ 1
293 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
IL17C	Interleukin 17C	0.9888	26
ATP12A	ATPase H+/K+ transporting non-gastric alpha2 subunit	0.9856	26
CXCL1	C-X-C motif chemokine ligand 1	0.9824	26
SERPINB4	Serpin family B member 4	0.9803	26
SERPINB3	Serpin family B member 3	0.9754	26
PGLYRP4	Peptidoglycan recognition protein 4	0.9750	26
CCL20	C-C motif chemokine ligand 20	0.9702	26
IL36G	Interleukin 36 gamma	0.9469	26
NMB	Neuromedin B	0.9417	26
TMEM45A	Transmembrane protein 45A	0.9409	26
BIK	BCL2 interacting killer	0.9347	26
SLPI	Secretory leukocyte peptidase inhibitor	0.9330	26
SPRR2D	Small proline rich protein 2D	0.9295	26
BPIFA2	BPI fold containing family A member 2	0.9244	26
IL36A	Interleukin 36 alpha	0.9228	26

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	0.1 nTPM
Breast	0.2 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	8.6 nTPM
Lung	8.6 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	7.4 nTPM
Colon	67.1 nTPM
Spleen	4.2 nTPM
Breast	2.6 nTPM
Liver	0.4 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Dendritic cells	0.5 nTPM
Breast	1.5 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM

Endothelial cells	3.0 nTPM
Prostate	17.1 nTPM
Breast	13.1 nTPM
Lung	6.2 nTPM
Pancreas	3.9 nTPM
Liver	0.9 nTPM
Endometrium	0.3 nTPM
Heart muscle	0.1 nTPM
Skin	0.1 nTPM
Eye	0.0 nTPM
Placenta	0.0 nTPM
Testis	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM

Fibroblasts	0.8 nTPM
Breast	4.5 nTPM
Prostate	2.6 nTPM
Placenta	1.0 nTPM
Adipose tissue	0.4 nTPM
Skin	0.3 nTPM
Esophagus	0.3 nTPM
Heart muscle	0.1 nTPM
Lung	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM
Stomach	0.0 nTPM

Intestinal goblet cells	31.8 nTPM
Colon	74.3 nTPM
Rectum	12.5 nTPM
Small intestine	8.6 nTPM

Macrophages	0.3 nTPM
Spleen	3.1 nTPM
Lung	0.9 nTPM
Endometrium	0.6 nTPM
Breast	0.6 nTPM
Kidney	0.0 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	219.6 nTPM
Colon	619.3 nTPM
Rectum	32.1 nTPM
Small intestine	7.5 nTPM

Plasma cells	0.2 nTPM
Spleen	0.7 nTPM
Stomach	0.4 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Respiratory ciliated cells	152.9 nTPM
Bronchus	305.9 nTPM
Lung	0.0 nTPM

Smooth muscle cells	50.5 nTPM
Bronchus	551.1 nTPM
Pancreas	2.3 nTPM
Prostate	1.3 nTPM
Breast	1.0 nTPM
Endometrium	0.2 nTPM
Heart muscle	0.1 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM

T-cells	2.5 nTPM
Colon	30.4 nTPM
Spleen	4.6 nTPM
Lung	4.5 nTPM
Breast	2.2 nTPM
Endometrium	0.7 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Prostate	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Ovary	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Basal prostatic cells	4.7 nTPM
Prostate	4.7 nTPM

Collecting duct cells	18.4 nTPM
Kidney	18.4 nTPM

Distal enterocytes	375.4 nTPM
Colon	428.1 nTPM
Rectum	322.7 nTPM

Exocrine glandular cells	317.3 nTPM
Pancreas	317.3 nTPM

Undifferentiated cells	154.1 nTPM
Colon	387.6 nTPM
Rectum	55.3 nTPM
Small intestine	19.3 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