Single cell type - IRF9 - 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.	IRF9
Gene descriptionⁱ Full gene name according to HGNC.	Interferon regulatory factor 9
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes 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.	5

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	Cell type enhanced (NK-cells)
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	Cell line enhanced (BJ hTERT+ SV40 Large T+, BJ hTERT+ SV40 Large T+ RasG12V, GAMG)
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 (NK-cells)

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

IRF9 is part of cluster 52 Non-specific - Transcription with confidenceⁱ 1
611 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
DDX39B	DExD-box helicase 39B	0.6934	52
TRIM56	Tripartite motif containing 56	0.6932	52
TRIM73	Tripartite motif containing 73	0.6698	40
SLC25A45	Solute carrier family 25 member 45	0.6651	63
TAS2R20	Taste 2 receptor member 20	0.6565	52
HELZ2	Helicase with zinc finger 2	0.6470	40
OR52H1	Olfactory receptor family 52 subfamily H member 1	0.6380	52
ALG1L2	ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase like 2	0.6284	40
ZNF431	Zinc finger protein 431	0.6205	52
XAF1	XIAP associated factor 1	0.6187	14
HSPG2	Heparan sulfate proteoglycan 2	0.6033	40
LDLRAD2	Low density lipoprotein receptor class A domain containing 2	0.5837	40
SLF2	SMC5-SMC6 complex localization factor 2	0.5805	52
ZNF224	Zinc finger protein 224	0.5767	52
GOLGA6L7	Golgin A6 family like 7	0.5725	40

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	37.9 nTPM
Breast	39.7 nTPM
Adipose tissue	36.1 nTPM

Alveolar cells type 1	25.6 nTPM
Lung	25.6 nTPM

Alveolar cells type 2	15.1 nTPM
Lung	15.1 nTPM

Astrocytes	21.2 nTPM
Brain	21.2 nTPM

B-cells	22.8 nTPM
PBMC	41.4 nTPM
Kidney	38.1 nTPM
Bone marrow	29.4 nTPM
Adipose tissue	28.1 nTPM
Spleen	23.9 nTPM
Breast	17.3 nTPM
Lymph node	15.2 nTPM
Liver	13.8 nTPM
Stomach	11.3 nTPM
Colon	9.6 nTPM

Dendritic cells	32.0 nTPM
PBMC	43.8 nTPM
Breast	27.4 nTPM
Adipose tissue	24.9 nTPM

Endothelial cells	21.0 nTPM
Skeletal muscle	57.6 nTPM
Ovary	30.8 nTPM
Eye	29.9 nTPM
Prostate	28.1 nTPM
Breast	27.7 nTPM
Endometrium	25.0 nTPM
Lung	18.7 nTPM
Testis	18.7 nTPM
Skin	14.5 nTPM
Esophagus	12.9 nTPM
Placenta	11.9 nTPM
Liver	11.0 nTPM
Heart muscle	6.7 nTPM
Pancreas	0.0 nTPM

Fibroblasts	14.8 nTPM
Ovary	39.4 nTPM
Lung	34.7 nTPM
Breast	20.7 nTPM
Skeletal muscle	19.5 nTPM
Stomach	11.9 nTPM
Skin	9.1 nTPM
Esophagus	8.3 nTPM
Adipose tissue	7.4 nTPM
Prostate	6.5 nTPM
Placenta	3.6 nTPM
Heart muscle	1.4 nTPM

Intestinal goblet cells	5.3 nTPM
Small intestine	11.5 nTPM
Colon	2.9 nTPM
Rectum	1.7 nTPM

Macrophages	13.4 nTPM
Lung	27.2 nTPM
Kidney	20.4 nTPM
Pancreas	20.4 nTPM
Bone marrow	20.0 nTPM
Ovary	17.9 nTPM
Skeletal muscle	17.4 nTPM
Endometrium	17.1 nTPM
Breast	12.2 nTPM
Prostate	11.5 nTPM
Spleen	10.4 nTPM
Testis	9.2 nTPM
Adipose tissue	7.9 nTPM
Stomach	5.9 nTPM
Esophagus	3.1 nTPM
PBMC	0.0 nTPM

Paneth cells	10.9 nTPM
Small intestine	22.5 nTPM
Colon	6.5 nTPM
Rectum	3.6 nTPM

Plasma cells	13.2 nTPM
Adipose tissue	28.5 nTPM
Stomach	15.1 nTPM
Bone marrow	11.5 nTPM
Spleen	10.7 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	32.3 nTPM
Lung	54.0 nTPM
Bronchus	10.6 nTPM

Smooth muscle cells	15.1 nTPM
Ovary	27.6 nTPM
Skeletal muscle	25.8 nTPM
Breast	25.0 nTPM
Endometrium	21.7 nTPM
Prostate	19.1 nTPM
Adipose tissue	16.4 nTPM
Skin	10.1 nTPM
Esophagus	9.3 nTPM
Heart muscle	9.0 nTPM
Pancreas	2.8 nTPM
Bronchus	0.0 nTPM

T-cells	26.1 nTPM
PBMC	66.3 nTPM
Kidney	62.9 nTPM
Lung	42.6 nTPM
Skeletal muscle	42.0 nTPM
Bone marrow	26.6 nTPM
Adipose tissue	25.3 nTPM
Ovary	24.5 nTPM
Endometrium	24.3 nTPM
Liver	21.5 nTPM
Breast	21.0 nTPM
Spleen	20.6 nTPM
Skin	17.5 nTPM
Lymph node	13.6 nTPM
Colon	13.3 nTPM
Stomach	10.2 nTPM
Esophagus	6.6 nTPM
Prostate	4.7 nTPM

Basal keratinocytes	2.3 nTPM
Skin	2.3 nTPM

Basal prostatic cells	8.6 nTPM
Prostate	8.6 nTPM

Basal respiratory cells	6.1 nTPM
Bronchus	6.1 nTPM

Basal squamous epithelial cells	6.2 nTPM
Esophagus	6.2 nTPM

Undifferentiated cells	4.9 nTPM
Small intestine	9.6 nTPM
Colon	2.8 nTPM
Rectum	2.2 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