Single cell type - GCN1 - 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.	GCN1
Gene descriptionⁱ Full gene name according to HGNC.	GCN1 activator of EIF2AK4
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	Intracellular
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	Non-specific - Transcription (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 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: 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

GCN1 is part of cluster 59 Non-specific - Transcription with confidenceⁱ 1
354 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
KMT5B	Lysine methyltransferase 5B	0.6669	59
FAAP100	FA core complex associated protein 100	0.5571	59
LDAH	Lipid droplet associated hydrolase	0.5311	59
PUM3	Pumilio RNA binding family member 3	0.5095	36
ZNF765	Zinc finger protein 765	0.5064	40
CRAMP1	Cramped chromatin regulator homolog 1	0.5000	59
PLOD1	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1	0.4916	38
VPS50	VPS50 subunit of EARP/GARPII complex	0.4913	66
DNAAF5	Dynein axonemal assembly factor 5	0.4810	59
MFSD14B	Major facilitator superfamily domain containing 14B	0.4785	19
LUC7L2	LUC7 like 2, pre-mRNA splicing factor	0.4722	59
SLF2	SMC5-SMC6 complex localization factor 2	0.4702	52
SMCR8	SMCR8-C9orf72 complex subunit	0.4511	19
PPP4R3B	Protein phosphatase 4 regulatory subunit 3B	0.4486	59
NCBP3	Nuclear cap binding subunit 3	0.4482	59

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	12.0 nTPM
Breast	13.3 nTPM
Adipose tissue	10.7 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	17.9 nTPM
Lung	17.9 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	11.2 nTPM
Bone marrow	20.4 nTPM
Liver	19.6 nTPM
Stomach	14.5 nTPM
PBMC	11.5 nTPM
Lymph node	11.4 nTPM
Adipose tissue	10.5 nTPM
Spleen	10.0 nTPM
Breast	9.4 nTPM
Kidney	4.8 nTPM
Colon	0.0 nTPM

Dendritic cells	12.0 nTPM
PBMC	16.0 nTPM
Breast	11.0 nTPM
Adipose tissue	9.2 nTPM

Endothelial cells	10.5 nTPM
Lung	18.7 nTPM
Esophagus	16.1 nTPM
Liver	15.6 nTPM
Ovary	13.7 nTPM
Endometrium	12.6 nTPM
Skeletal muscle	12.5 nTPM
Pancreas	11.6 nTPM
Breast	10.6 nTPM
Placenta	10.2 nTPM
Testis	9.8 nTPM
Prostate	9.3 nTPM
Eye	5.7 nTPM
Heart muscle	0.0 nTPM
Skin	0.0 nTPM

Fibroblasts	10.5 nTPM
Ovary	22.0 nTPM
Skeletal muscle	15.0 nTPM
Stomach	14.9 nTPM
Placenta	13.7 nTPM
Lung	13.4 nTPM
Breast	10.2 nTPM
Prostate	9.3 nTPM
Adipose tissue	8.6 nTPM
Esophagus	8.6 nTPM
Heart muscle	0.0 nTPM
Skin	0.0 nTPM

Intestinal goblet cells	11.4 nTPM
Small intestine	17.5 nTPM
Rectum	16.6 nTPM
Colon	0.0 nTPM

Macrophages	8.9 nTPM
Lung	22.9 nTPM
Esophagus	14.2 nTPM
Bone marrow	13.8 nTPM
PBMC	13.6 nTPM
Spleen	10.4 nTPM
Skeletal muscle	9.6 nTPM
Breast	9.0 nTPM
Ovary	8.9 nTPM
Adipose tissue	7.5 nTPM
Endometrium	6.8 nTPM
Kidney	6.1 nTPM
Testis	5.8 nTPM
Stomach	2.9 nTPM
Prostate	1.2 nTPM
Pancreas	0.0 nTPM

Paneth cells	8.6 nTPM
Rectum	14.7 nTPM
Small intestine	11.3 nTPM
Colon	0.0 nTPM

Plasma cells	17.7 nTPM
Spleen	29.0 nTPM
Stomach	21.6 nTPM
Bone marrow	21.4 nTPM
Adipose tissue	10.3 nTPM
Esophagus	6.1 nTPM

Respiratory ciliated cells	2.9 nTPM
Lung	5.8 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	8.9 nTPM
Ovary	17.0 nTPM
Pancreas	14.4 nTPM
Skeletal muscle	13.7 nTPM
Endometrium	13.3 nTPM
Breast	12.0 nTPM
Esophagus	10.9 nTPM
Adipose tissue	10.6 nTPM
Prostate	6.5 nTPM
Heart muscle	0.0 nTPM
Skin	0.0 nTPM
Bronchus	0.0 nTPM

T-cells	10.1 nTPM
Lung	22.8 nTPM
Stomach	14.8 nTPM
Bone marrow	14.5 nTPM
PBMC	13.8 nTPM
Breast	13.2 nTPM
Lymph node	12.7 nTPM
Skeletal muscle	11.6 nTPM
Spleen	11.4 nTPM
Liver	10.8 nTPM
Endometrium	10.8 nTPM
Adipose tissue	10.4 nTPM
Kidney	7.5 nTPM
Ovary	6.7 nTPM
Esophagus	6.6 nTPM
Prostate	4.7 nTPM
Colon	0.0 nTPM
Skin	0.0 nTPM

Cholangiocytes	12.8 nTPM
Liver	12.8 nTPM

Distal tubular cells	1.9 nTPM
Kidney	1.9 nTPM

Early spermatids	1.9 nTPM
Testis	1.9 nTPM

Endometrial stromal cells	14.1 nTPM
Endometrium	14.1 nTPM

Undifferentiated cells	11.7 nTPM
Rectum	18.9 nTPM
Small intestine	16.1 nTPM
Colon	0.0 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