Single cell type - PCM1 - 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.	PCM1
Gene descriptionⁱ Full gene name according to HGNC.	Pericentriolar material 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Cancer-related genes Disease 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	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	7

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	Spermatocytes - Spermatogenesis (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 (Spermatocytes, Early spermatids)
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: Cell type enhanced (Spermatocytes, Early spermatids)

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

PCM1 is part of cluster 66 Spermatocytes - Spermatogenesis with confidenceⁱ 1
507 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
CEP63	Centrosomal protein 63	0.5680	66
CLGN	Calmegin	0.5308	66
GBX1	Gastrulation brain homeobox 1	0.5294	66
CFAP58	Cilia and flagella associated protein 58	0.5209	49
CIR1	Corepressor interacting with RBPJ, CIR1	0.5157	66
LYRM7	LYR motif containing 7	0.5135	66
BRD8	Bromodomain containing 8	0.5127	66
CNTRL	Centriolin	0.5059	66
ARL14EP	ADP ribosylation factor like GTPase 14 effector protein	0.4964	66
TCEANC2	Transcription elongation factor A N-terminal and central domain containing 2	0.4949	13
C18orf21	Chromosome 18 open reading frame 21	0.4902	66
CEP83	Centrosomal protein 83	0.4884	49
ORC2	Origin recognition complex subunit 2	0.4878	66
NEU3	Neuraminidase 3	0.4804	9
ZNF544	Zinc finger protein 544	0.4798	9

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	91.6 nTPM
Adipose tissue	102.9 nTPM
Breast	80.2 nTPM

Alveolar cells type 1	128.2 nTPM
Lung	128.2 nTPM

Alveolar cells type 2	154.9 nTPM
Lung	154.9 nTPM

Astrocytes	187.7 nTPM
Brain	187.7 nTPM

B-cells	109.3 nTPM
Adipose tissue	185.5 nTPM
PBMC	147.0 nTPM
Lymph node	141.3 nTPM
Stomach	121.2 nTPM
Spleen	112.8 nTPM
Colon	110.2 nTPM
Bone marrow	103.8 nTPM
Breast	89.6 nTPM
Kidney	42.9 nTPM
Liver	38.6 nTPM

Dendritic cells	145.9 nTPM
PBMC	183.3 nTPM
Adipose tissue	166.5 nTPM
Breast	87.9 nTPM

Endothelial cells	86.5 nTPM
Lung	174.6 nTPM
Heart muscle	145.0 nTPM
Skeletal muscle	111.9 nTPM
Endometrium	105.6 nTPM
Eye	93.8 nTPM
Ovary	82.3 nTPM
Testis	79.7 nTPM
Breast	73.7 nTPM
Liver	70.6 nTPM
Esophagus	70.2 nTPM
Pancreas	57.9 nTPM
Prostate	52.9 nTPM
Placenta	50.1 nTPM
Skin	42.6 nTPM

Erythroid cells	115.5 nTPM
Bone marrow	145.4 nTPM
Liver	85.5 nTPM

Fibroblasts	100.4 nTPM
Lung	254.7 nTPM
Heart muscle	151.6 nTPM
Skeletal muscle	104.3 nTPM
Adipose tissue	103.3 nTPM
Esophagus	89.8 nTPM
Breast	87.8 nTPM
Ovary	82.5 nTPM
Stomach	71.3 nTPM
Prostate	64.6 nTPM
Skin	50.5 nTPM
Placenta	44.1 nTPM

Intestinal goblet cells	45.7 nTPM
Small intestine	48.7 nTPM
Rectum	46.8 nTPM
Colon	41.4 nTPM

Macrophages	83.6 nTPM
Lung	122.0 nTPM
Adipose tissue	105.8 nTPM
Ovary	104.1 nTPM
Esophagus	102.2 nTPM
Endometrium	89.2 nTPM
Testis	87.8 nTPM
Bone marrow	85.0 nTPM
Stomach	85.0 nTPM
Spleen	82.9 nTPM
Prostate	82.6 nTPM
Skeletal muscle	80.0 nTPM
Breast	76.6 nTPM
Kidney	56.0 nTPM
Pancreas	53.7 nTPM
PBMC	40.9 nTPM

Paneth cells	36.0 nTPM
Small intestine	45.0 nTPM
Rectum	43.4 nTPM
Colon	19.7 nTPM

Plasma cells	84.7 nTPM
Adipose tissue	190.9 nTPM
Esophagus	67.8 nTPM
Stomach	64.0 nTPM
Spleen	61.1 nTPM
Bone marrow	39.5 nTPM

Respiratory ciliated cells	282.1 nTPM
Lung	427.0 nTPM
Bronchus	137.2 nTPM

Smooth muscle cells	92.7 nTPM
Heart muscle	155.0 nTPM
Endometrium	125.2 nTPM
Adipose tissue	122.8 nTPM
Skeletal muscle	120.6 nTPM
Ovary	106.1 nTPM
Breast	93.3 nTPM
Esophagus	88.3 nTPM
Prostate	72.2 nTPM
Skin	52.0 nTPM
Bronchus	43.3 nTPM
Pancreas	41.0 nTPM

Basal keratinocytes	33.8 nTPM
Skin	33.8 nTPM

Basal prostatic cells	66.3 nTPM
Prostate	66.3 nTPM

Basal respiratory cells	44.4 nTPM
Bronchus	44.4 nTPM

Basal squamous epithelial cells	75.7 nTPM
Esophagus	75.7 nTPM

T-cells	122.5 nTPM
Adipose tissue	208.3 nTPM
Skeletal muscle	195.0 nTPM
Lung	180.8 nTPM
PBMC	169.7 nTPM
Endometrium	147.9 nTPM
Lymph node	138.7 nTPM
Stomach	119.5 nTPM
Breast	108.5 nTPM
Spleen	103.4 nTPM
Esophagus	98.3 nTPM
Colon	97.4 nTPM
Bone marrow	97.3 nTPM
Prostate	94.7 nTPM
Liver	93.5 nTPM
Ovary	80.1 nTPM
Kidney	76.0 nTPM
Skin	73.7 nTPM

Undifferentiated cells	50.6 nTPM
Colon	52.6 nTPM
Rectum	50.1 nTPM
Small intestine	49.2 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