Single cell type - PHTF1 - 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.	PHTF1
Gene descriptionⁱ Full gene name according to HGNC.	Putative homeodomain transcription factor 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Plasma proteins Transcription factors
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	Membrane
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	Ciliated cells - Cilium 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 (Early spermatids, Spermatocytes, Late spermatids, Inhibitory neurons, Excitatory neurons)
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 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 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

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 (Early spermatids, Spermatocytes, Late spermatids, Inhibitory neurons, Excitatory neurons)

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

PHTF1 is part of cluster 49 Ciliated cells - Cilium organization with confidenceⁱ 1
457 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
ANKRD42	Ankyrin repeat domain 42	0.5331	49
SPAG16	Sperm associated antigen 16	0.4743	49
DNAL1	Dynein axonemal light chain 1	0.4699	49
CCDC138	Coiled-coil domain containing 138	0.4658	23
KIF27	Kinesin family member 27	0.4616	49
IQCH	IQ motif containing H	0.4564	49
IQUB	IQ motif and ubiquitin domain containing	0.4481	49
CCDC148	Coiled-coil domain containing 148	0.4429	9
TTC26	Tetratricopeptide repeat domain 26	0.4398	49
ARMC3	Armadillo repeat containing 3	0.4380	49
OPN5	Opsin 5	0.4342	25
HTR7	5-hydroxytryptamine receptor 7	0.4318	8
ZNF555	Zinc finger protein 555	0.4294	66
CCDC181	Coiled-coil domain containing 181	0.4274	49
LETM2	Leucine zipper and EF-hand containing transmembrane protein 2	0.4244	66

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	12.5 nTPM
Breast	13.3 nTPM
Adipose tissue	11.5 nTPM

Alveolar cells type 1	6.4 nTPM
Lung	6.4 nTPM

Alveolar cells type 2	10.5 nTPM
Lung	10.5 nTPM

Astrocytes	34.3 nTPM
Brain	34.3 nTPM

B-cells	16.7 nTPM
Liver	26.7 nTPM
Stomach	24.1 nTPM
Kidney	23.8 nTPM
Colon	22.3 nTPM
Spleen	19.4 nTPM
Adipose tissue	18.0 nTPM
Lymph node	16.7 nTPM
Breast	10.7 nTPM
Bone marrow	4.1 nTPM
PBMC	1.4 nTPM

Dendritic cells	22.9 nTPM
Breast	34.6 nTPM
Adipose tissue	30.0 nTPM
PBMC	4.0 nTPM

Endothelial cells	19.7 nTPM
Pancreas	38.6 nTPM
Lung	24.9 nTPM
Prostate	24.4 nTPM
Eye	23.5 nTPM
Endometrium	21.8 nTPM
Heart muscle	20.5 nTPM
Ovary	19.7 nTPM
Esophagus	18.6 nTPM
Skin	18.4 nTPM
Breast	16.5 nTPM
Placenta	15.9 nTPM
Testis	15.4 nTPM
Skeletal muscle	13.7 nTPM
Liver	3.7 nTPM

Fibroblasts	10.8 nTPM
Stomach	13.4 nTPM
Skin	13.3 nTPM
Placenta	13.2 nTPM
Prostate	12.9 nTPM
Ovary	12.4 nTPM
Breast	12.0 nTPM
Skeletal muscle	11.8 nTPM
Esophagus	10.8 nTPM
Adipose tissue	7.1 nTPM
Lung	6.7 nTPM
Heart muscle	5.6 nTPM

Intestinal goblet cells	3.1 nTPM
Colon	3.6 nTPM
Small intestine	3.5 nTPM
Rectum	2.2 nTPM

Macrophages	18.0 nTPM
PBMC	40.9 nTPM
Breast	29.4 nTPM
Prostate	24.1 nTPM
Esophagus	22.0 nTPM
Adipose tissue	20.3 nTPM
Skeletal muscle	19.3 nTPM
Spleen	17.6 nTPM
Ovary	17.1 nTPM
Endometrium	16.4 nTPM
Bone marrow	12.5 nTPM
Testis	11.7 nTPM
Stomach	11.7 nTPM
Kidney	9.9 nTPM
Lung	8.9 nTPM
Pancreas	7.7 nTPM

Paneth cells	1.2 nTPM
Rectum	3.6 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Plasma cells	31.0 nTPM
Stomach	53.1 nTPM
Spleen	46.2 nTPM
Adipose tissue	31.6 nTPM
Bone marrow	18.2 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	58.7 nTPM
Bronchus	63.4 nTPM
Lung	54.0 nTPM

Smooth muscle cells	12.2 nTPM
Bronchus	21.6 nTPM
Endometrium	16.4 nTPM
Ovary	15.5 nTPM
Skin	15.0 nTPM
Pancreas	13.2 nTPM
Prostate	13.1 nTPM
Breast	10.1 nTPM
Heart muscle	8.4 nTPM
Skeletal muscle	7.9 nTPM
Esophagus	7.8 nTPM
Adipose tissue	5.8 nTPM

T-cells	23.1 nTPM
Stomach	43.2 nTPM
Prostate	42.6 nTPM
Breast	37.4 nTPM
Adipose tissue	30.9 nTPM
Skeletal muscle	29.8 nTPM
Liver	27.4 nTPM
Endometrium	26.9 nTPM
Colon	23.3 nTPM
Spleen	22.3 nTPM
Skin	20.7 nTPM
Ovary	20.1 nTPM
Kidney	17.8 nTPM
Bone marrow	16.5 nTPM
Lymph node	14.8 nTPM
Esophagus	13.1 nTPM
PBMC	3.6 nTPM
Lung	1.5 nTPM

Basal keratinocytes	2.4 nTPM
Skin	2.4 nTPM

Basal prostatic cells	6.8 nTPM
Prostate	6.8 nTPM

Basal squamous epithelial cells	6.8 nTPM
Esophagus	6.8 nTPM

Cholangiocytes	14.3 nTPM
Liver	14.3 nTPM

Undifferentiated cells	4.6 nTPM
Colon	6.8 nTPM
Small intestine	3.6 nTPM
Rectum	3.5 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