Single cell type - FAM53C - 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.	FAM53C
Gene descriptionⁱ Full gene name according to HGNC.	Family with sequence similarity 53 member C
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.	4

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	Spermatids - 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	Group enriched (Late spermatids, 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	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 many
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: Group enriched (Late spermatids, 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

FAM53C is part of cluster 31 Spermatids - Spermatogenesis with confidenceⁱ 1
413 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
LMNTD2	Lamin tail domain containing 2	0.5765	31
DALRD3	DALR anticodon binding domain containing 3	0.5585	31
ZNF567	Zinc finger protein 567	0.5414	31
DNAJA4	DnaJ heat shock protein family (Hsp40) member A4	0.5359	34
BRD4	Bromodomain containing 4	0.5319	31
C11orf1	Chromosome 11 open reading frame 1	0.5313	31
DDX3X	DEAD-box helicase 3 X-linked	0.5240	7
SEMG2	Semenogelin 2	0.5210	22
CCDC9	Coiled-coil domain containing 9	0.5191	31
RNF133	Ring finger protein 133	0.5180	31
FUZ	Fuzzy planar cell polarity protein	0.5177	31
FAM71C	Family with sequence similarity 71 member C	0.5158	31
TESK1	Testis associated actin remodelling kinase 1	0.5129	41
GTSF1L	Gametocyte specific factor 1 like	0.5115	31
CSTL1	Cystatin like 1	0.5069	31

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	27.1 nTPM
Breast	29.8 nTPM
Adipose tissue	24.3 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	11.5 nTPM
Lung	11.5 nTPM

Astrocytes	19.6 nTPM
Brain	19.6 nTPM

B-cells	45.0 nTPM
Adipose tissue	80.7 nTPM
Colon	75.1 nTPM
Breast	68.3 nTPM
Spleen	63.0 nTPM
Lymph node	50.3 nTPM
Stomach	38.6 nTPM
Liver	26.3 nTPM
Kidney	19.0 nTPM
PBMC	18.6 nTPM
Bone marrow	10.6 nTPM

Dendritic cells	54.5 nTPM
Breast	84.2 nTPM
Adipose tissue	55.3 nTPM
PBMC	23.9 nTPM

Endothelial cells	24.9 nTPM
Eye	110.8 nTPM
Skeletal muscle	29.8 nTPM
Prostate	29.3 nTPM
Breast	26.7 nTPM
Liver	25.7 nTPM
Ovary	20.7 nTPM
Skin	20.2 nTPM
Testis	17.7 nTPM
Endometrium	17.5 nTPM
Placenta	16.5 nTPM
Esophagus	12.4 nTPM
Lung	9.3 nTPM
Heart muscle	7.9 nTPM
Pancreas	3.9 nTPM

Fibroblasts	26.2 nTPM
Stomach	53.4 nTPM
Adipose tissue	40.3 nTPM
Prostate	35.4 nTPM
Skeletal muscle	29.6 nTPM
Breast	27.6 nTPM
Esophagus	25.5 nTPM
Skin	23.8 nTPM
Ovary	20.3 nTPM
Placenta	14.0 nTPM
Heart muscle	11.6 nTPM
Lung	6.7 nTPM

Intestinal goblet cells	34.5 nTPM
Colon	49.4 nTPM
Small intestine	34.9 nTPM
Rectum	19.1 nTPM

Macrophages	43.1 nTPM
Breast	97.0 nTPM
Spleen	82.0 nTPM
Adipose tissue	76.4 nTPM
Skeletal muscle	61.6 nTPM
Stomach	61.5 nTPM
Esophagus	51.9 nTPM
Testis	41.8 nTPM
Endometrium	39.3 nTPM
Ovary	36.0 nTPM
Prostate	31.0 nTPM
Bone marrow	20.0 nTPM
Kidney	19.6 nTPM
Pancreas	15.3 nTPM
Lung	13.1 nTPM
PBMC	0.0 nTPM

Paneth cells	35.3 nTPM
Colon	39.6 nTPM
Small intestine	37.6 nTPM
Rectum	28.7 nTPM

Plasma cells	28.1 nTPM
Adipose tissue	51.6 nTPM
Spleen	35.5 nTPM
Stomach	30.8 nTPM
Bone marrow	16.5 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	24.3 nTPM
Bronchus	38.5 nTPM
Lung	10.2 nTPM

Smooth muscle cells	24.2 nTPM
Skeletal muscle	41.9 nTPM
Prostate	41.6 nTPM
Skin	33.4 nTPM
Breast	31.4 nTPM
Adipose tissue	31.1 nTPM
Ovary	25.9 nTPM
Endometrium	17.6 nTPM
Bronchus	13.3 nTPM
Esophagus	12.4 nTPM
Pancreas	9.4 nTPM
Heart muscle	8.1 nTPM

T-cells	43.2 nTPM
Breast	92.4 nTPM
Colon	84.1 nTPM
Spleen	70.1 nTPM
Adipose tissue	63.0 nTPM
Skeletal muscle	62.7 nTPM
Ovary	46.7 nTPM
Liver	45.4 nTPM
Skin	40.6 nTPM
Stomach	38.7 nTPM
Lymph node	36.5 nTPM
Endometrium	33.1 nTPM
Kidney	30.2 nTPM
Esophagus	26.2 nTPM
Prostate	23.6 nTPM
PBMC	15.9 nTPM
Lung	13.6 nTPM
Bone marrow	11.0 nTPM

Basal keratinocytes	25.0 nTPM
Skin	25.0 nTPM

Basal prostatic cells	27.2 nTPM
Prostate	27.2 nTPM

Basal squamous epithelial cells	37.0 nTPM
Esophagus	37.0 nTPM

Cholangiocytes	10.0 nTPM
Liver	10.0 nTPM

Undifferentiated cells	33.3 nTPM
Colon	45.1 nTPM
Rectum	28.5 nTPM
Small intestine	26.4 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