Single cell type - IGHA1 - 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.	IGHA1
Gene descriptionⁱ Full gene name according to HGNC.	Immunoglobulin heavy constant alpha 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Immunoglobulin genes
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,Membrane,Secreted
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	Plasma cells - Humoral immune response (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 (Plasma cells, B-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	Group enriched (memory B-cell, naive B-cell)
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	Cell line enhanced (HDLM-2, RPMI-8226, SH-SY5Y, U-266/70, U-266/84)
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
Extracellular locationⁱ A possible secretion of the protein was predicted based on N-terminal signal sequence (signal peptide) predictions and transmembrane region predictions, and subsequently annotated for its local or systemic secretion based on literature, function, and protein and RNA expression data. Read more	Protein predicted to be secreted

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 (Plasma cells, B-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

IGHA1 is part of cluster 55 Plasma cells - Humoral immune response with confidenceⁱ 1
379 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
IGHA2	Immunoglobulin heavy constant alpha 2 (A2m marker)	0.9637	55
TNFRSF17	TNF receptor superfamily member 17	0.8759	55
JCHAIN	Joining chain of multimeric IgA and IgM	0.8243	55
IGLV2-14	Immunoglobulin lambda variable 2-14	0.8194	55
IGLV1-51	Immunoglobulin lambda variable 1-51	0.8192	55
IGHV3-23	Immunoglobulin heavy variable 3-23	0.8179	55
IGLV2-23	Immunoglobulin lambda variable 2-23	0.8124	55
IGLV3-21	Immunoglobulin lambda variable 3-21	0.8109	55
IGLV1-47	Immunoglobulin lambda variable 1-47	0.8108	55
DERL3	Derlin 3	0.8104	55
IGHV1-2	Immunoglobulin heavy variable 1-2	0.8095	55
IGKV2-28	Immunoglobulin kappa variable 2-28	0.8075	55
IGLV3-25	Immunoglobulin lambda variable 3-25	0.8074	55
IGHV3-33	Immunoglobulin heavy variable 3-33	0.8073	55
IGLV6-57	Immunoglobulin lambda variable 6-57	0.8072	55

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	11.8 nTPM
Breast	20.0 nTPM
Adipose tissue	3.6 nTPM

Alveolar cells type 1	131.4 nTPM
Lung	131.4 nTPM

Alveolar cells type 2	783.5 nTPM
Lung	783.5 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

Basal keratinocytes	0.0 nTPM
Skin	0.0 nTPM

B-cells	17763.5 nTPM
Breast	143282.0 nTPM
Liver	32869.0 nTPM
Stomach	409.2 nTPM
Bone marrow	224.0 nTPM
Adipose tissue	200.1 nTPM
Kidney	185.7 nTPM
Colon	142.2 nTPM
Lymph node	120.6 nTPM
PBMC	111.3 nTPM
Spleen	91.1 nTPM

Dendritic cells	55.5 nTPM
Adipose tissue	125.2 nTPM
Breast	41.2 nTPM
PBMC	0.0 nTPM

Endothelial cells	26.5 nTPM
Lung	149.7 nTPM
Breast	119.4 nTPM
Esophagus	53.4 nTPM
Liver	37.6 nTPM
Heart muscle	4.9 nTPM
Skeletal muscle	3.1 nTPM
Placenta	2.2 nTPM
Prostate	0.4 nTPM
Endometrium	0.3 nTPM
Ovary	0.1 nTPM
Eye	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM

Fibroblasts	56.5 nTPM
Placenta	146.8 nTPM
Adipose tissue	137.3 nTPM
Breast	132.0 nTPM
Lung	101.7 nTPM
Stomach	62.4 nTPM
Esophagus	39.0 nTPM
Skeletal muscle	1.8 nTPM
Heart muscle	0.5 nTPM
Prostate	0.2 nTPM
Skin	0.0 nTPM
Ovary	0.0 nTPM

Intestinal goblet cells	13.6 nTPM
Rectum	28.0 nTPM
Colon	12.9 nTPM
Small intestine	0.0 nTPM

Macrophages	34.6 nTPM
Lung	342.3 nTPM
Stomach	93.7 nTPM
Breast	37.8 nTPM
PBMC	13.6 nTPM
Spleen	8.3 nTPM
Endometrium	5.8 nTPM
Skeletal muscle	4.9 nTPM
Adipose tissue	4.1 nTPM
Esophagus	3.1 nTPM
Bone marrow	2.5 nTPM
Kidney	2.3 nTPM
Prostate	1.2 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Ovary	0.0 nTPM

Paneth cells	12.8 nTPM
Rectum	28.5 nTPM
Colon	9.9 nTPM
Small intestine	0.0 nTPM

Plasma cells	34095.8 nTPM
Stomach	61812.3 nTPM
Adipose tissue	56142.1 nTPM
Esophagus	40143.2 nTPM
Bone marrow	6877.0 nTPM
Spleen	5504.3 nTPM

Respiratory ciliated cells	16.0 nTPM
Lung	32.1 nTPM
Bronchus	0.0 nTPM

Smooth muscle cells	13.6 nTPM
Heart muscle	94.5 nTPM
Esophagus	37.2 nTPM
Breast	9.6 nTPM
Skeletal muscle	5.0 nTPM
Adipose tissue	2.3 nTPM
Prostate	0.4 nTPM
Endometrium	0.1 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Bronchus	0.0 nTPM
Ovary	0.0 nTPM

Cholangiocytes	22.8 nTPM
Liver	22.8 nTPM

Cytotrophoblasts	0.7 nTPM
Placenta	0.7 nTPM

T-cells	2514.2 nTPM
Prostate	22926.1 nTPM
Lung	16546.4 nTPM
Breast	1501.8 nTPM
Skeletal muscle	833.9 nTPM
PBMC	418.0 nTPM
Ovary	204.6 nTPM
Stomach	126.4 nTPM
Liver	111.4 nTPM
Colon	23.7 nTPM
Esophagus	13.1 nTPM
Spleen	9.9 nTPM
Kidney	8.2 nTPM
Adipose tissue	6.4 nTPM
Bone marrow	6.2 nTPM
Lymph node	3.7 nTPM
Endometrium	2.1 nTPM
Skin	0.0 nTPM

Undifferentiated cells	27.9 nTPM
Colon	65.1 nTPM
Rectum	18.8 nTPM
Small intestine	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