Single cell type - NFX1 - 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.	NFX1
Gene descriptionⁱ Full gene name according to HGNC.	Nuclear transcription factor, X-box binding 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	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	2

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	Early 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	Low cell type specificity
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: Low cell type specificity

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

NFX1 is part of cluster 29 Early spermatids - Spermatogenesis with confidenceⁱ 1
337 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
EDRF1	Erythroid differentiation regulatory factor 1	0.5539	29
AGAP4	ArfGAP with GTPase domain, ankyrin repeat and PH domain 4	0.5389	29
AP5M1	Adaptor related protein complex 5 subunit mu 1	0.4924	29
QPCTL	Glutaminyl-peptide cyclotransferase like	0.4895	55
KLHL11	Kelch like family member 11	0.4876	29
ITFG2	Integrin alpha FG-GAP repeat containing 2	0.4819	52
ZNF721	Zinc finger protein 721	0.4587	52
EPS15L1	Epidermal growth factor receptor pathway substrate 15 like 1	0.4563	29
SENP2	SUMO specific peptidase 2	0.4446	29
CEP76	Centrosomal protein 76	0.4410	29
DESI1	Desumoylating isopeptidase 1	0.4408	29
CYP51A1	Cytochrome P450 family 51 subfamily A member 1	0.4404	11
CALCOCO2	Calcium binding and coiled-coil domain 2	0.4398	29
SNX31	Sorting nexin 31	0.4322	29
LTN1	Listerin E3 ubiquitin protein ligase 1	0.4319	29

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	16.0 nTPM
Adipose tissue	18.3 nTPM
Breast	13.6 nTPM

Alveolar cells type 1	60.9 nTPM
Lung	60.9 nTPM

Alveolar cells type 2	42.5 nTPM
Lung	42.5 nTPM

Astrocytes	35.3 nTPM
Brain	35.3 nTPM

B-cells	41.9 nTPM
Stomach	60.9 nTPM
Bone marrow	54.8 nTPM
Lymph node	50.8 nTPM
Adipose tissue	45.6 nTPM
Colon	43.2 nTPM
PBMC	35.7 nTPM
Spleen	34.3 nTPM
Kidney	33.4 nTPM
Liver	32.4 nTPM
Breast	28.1 nTPM

Dendritic cells	17.2 nTPM
Adipose tissue	20.4 nTPM
PBMC	16.0 nTPM
Breast	15.3 nTPM

Endothelial cells	14.9 nTPM
Heart muscle	33.2 nTPM
Esophagus	19.9 nTPM
Testis	19.8 nTPM
Eye	18.6 nTPM
Skeletal muscle	18.6 nTPM
Liver	17.4 nTPM
Ovary	14.9 nTPM
Endometrium	13.8 nTPM
Lung	12.5 nTPM
Breast	11.7 nTPM
Prostate	10.5 nTPM
Skin	9.6 nTPM
Placenta	8.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	18.5 nTPM
Esophagus	27.1 nTPM
Stomach	25.3 nTPM
Heart muscle	24.2 nTPM
Lung	22.4 nTPM
Adipose tissue	20.6 nTPM
Skeletal muscle	18.7 nTPM
Ovary	16.3 nTPM
Placenta	15.5 nTPM
Breast	15.0 nTPM
Prostate	11.2 nTPM
Skin	7.2 nTPM

Intestinal goblet cells	23.9 nTPM
Colon	31.5 nTPM
Rectum	27.0 nTPM
Small intestine	13.4 nTPM

Macrophages	19.0 nTPM
Lung	42.1 nTPM
Ovary	25.6 nTPM
Skeletal muscle	22.8 nTPM
Spleen	21.8 nTPM
Adipose tissue	21.6 nTPM
Bone marrow	21.2 nTPM
Testis	20.9 nTPM
Esophagus	20.4 nTPM
Breast	18.9 nTPM
Endometrium	14.3 nTPM
Prostate	13.8 nTPM
PBMC	13.6 nTPM
Pancreas	10.2 nTPM
Kidney	9.1 nTPM
Stomach	8.8 nTPM

Paneth cells	21.6 nTPM
Colon	26.4 nTPM
Rectum	19.5 nTPM
Small intestine	18.8 nTPM

Plasma cells	47.1 nTPM
Stomach	72.3 nTPM
Esophagus	55.5 nTPM
Bone marrow	47.7 nTPM
Spleen	36.5 nTPM
Adipose tissue	23.3 nTPM

Respiratory ciliated cells	43.7 nTPM
Lung	58.3 nTPM
Bronchus	29.1 nTPM

Smooth muscle cells	17.5 nTPM
Heart muscle	47.5 nTPM
Esophagus	20.1 nTPM
Skeletal muscle	19.8 nTPM
Adipose tissue	18.8 nTPM
Breast	16.4 nTPM
Pancreas	14.6 nTPM
Endometrium	14.3 nTPM
Bronchus	13.3 nTPM
Prostate	12.5 nTPM
Ovary	10.9 nTPM
Skin	4.9 nTPM

T-cells	20.9 nTPM
Lung	50.1 nTPM
Bone marrow	31.4 nTPM
Lymph node	30.4 nTPM
PBMC	30.0 nTPM
Spleen	24.6 nTPM
Adipose tissue	20.9 nTPM
Stomach	20.4 nTPM
Liver	19.0 nTPM
Skeletal muscle	18.2 nTPM
Ovary	17.8 nTPM
Breast	17.8 nTPM
Endometrium	15.7 nTPM
Colon	14.2 nTPM
Skin	13.8 nTPM
Kidney	13.1 nTPM
Esophagus	13.1 nTPM
Prostate	4.7 nTPM

Basal keratinocytes	8.4 nTPM
Skin	8.4 nTPM

Collecting duct cells	27.6 nTPM
Kidney	27.6 nTPM

Cone photoreceptor cells	54.2 nTPM
Eye	54.2 nTPM

Distal tubular cells	7.9 nTPM
Kidney	7.9 nTPM

Undifferentiated cells	16.7 nTPM
Rectum	19.5 nTPM
Small intestine	17.7 nTPM
Colon	12.8 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