Single cell type - SMAD9 - 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.	SMAD9
Gene descriptionⁱ Full gene name according to HGNC.	SMAD family member 9
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Human 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.	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	Endometrium - 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 (Glandular and luminal cells, Enteroendocrine cells, Astrocytes, Hepatic stellate 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	Not detected in immune cells
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	Not detected
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 (fHDF/TERT166, HEK93, SH-SY5Y)
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 (Glandular and luminal cells, Enteroendocrine cells, Astrocytes, Hepatic stellate 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

SMAD9 is part of cluster 44 Endometrium - Transcription with confidenceⁱ 1
491 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
BCL9	BCL9 transcription coactivator	0.7023	44
PHACTR4	Phosphatase and actin regulator 4	0.6883	44
CNKSR3	CNKSR family member 3	0.6746	44
PKHD1L1	PKHD1 like 1	0.6650	44
ITGB8	Integrin subunit beta 8	0.6561	44
MMP26	Matrix metallopeptidase 26	0.6450	44
SPAG11B	Sperm associated antigen 11B	0.6363	44
POU5F1	POU class 5 homeobox 1	0.6316	44
ALPG	Alkaline phosphatase, germ cell	0.6252	44
ELP3	Elongator acetyltransferase complex subunit 3	0.6194	44
HAP1	Huntingtin associated protein 1	0.6176	44
FBXO21	F-box protein 21	0.6154	44
AL353572.3	Novel protein	0.6085	44
MFHAS1	Malignant fibrous histiocytoma amplified sequence 1	0.6063	44
MID1	Midline 1	0.6032	64

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	22.5 nTPM
Adipose tissue	24.6 nTPM
Breast	20.4 nTPM

Alveolar cells type 1	28.9 nTPM
Lung	28.9 nTPM

Alveolar cells type 2	11.5 nTPM
Lung	11.5 nTPM

B-cells	0.4 nTPM
Breast	2.6 nTPM
Liver	1.3 nTPM
Lymph node	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Basal keratinocytes	2.8 nTPM
Skin	2.8 nTPM

Dendritic cells	0.2 nTPM
Breast	0.4 nTPM
Adipose tissue	0.3 nTPM
PBMC	0.0 nTPM

Endothelial cells	26.7 nTPM
Esophagus	68.5 nTPM
Liver	64.2 nTPM
Lung	31.2 nTPM
Eye	29.1 nTPM
Prostate	24.6 nTPM
Heart muscle	24.3 nTPM
Breast	24.2 nTPM
Placenta	22.7 nTPM
Skin	19.6 nTPM
Skeletal muscle	18.7 nTPM
Pancreas	15.5 nTPM
Endometrium	15.2 nTPM
Ovary	9.1 nTPM
Testis	6.2 nTPM

Fibroblasts	11.6 nTPM
Heart muscle	31.2 nTPM
Stomach	22.3 nTPM
Prostate	12.7 nTPM
Adipose tissue	11.3 nTPM
Skeletal muscle	8.0 nTPM
Skin	7.7 nTPM
Ovary	7.6 nTPM
Breast	7.2 nTPM
Placenta	7.0 nTPM
Esophagus	6.6 nTPM
Lung	5.6 nTPM

Intestinal goblet cells	15.6 nTPM
Colon	20.8 nTPM
Rectum	19.4 nTPM
Small intestine	6.6 nTPM

Macrophages	1.1 nTPM
Endometrium	9.9 nTPM
Skeletal muscle	1.6 nTPM
Esophagus	1.6 nTPM
Prostate	1.2 nTPM
Ovary	0.9 nTPM
Breast	0.4 nTPM
Adipose tissue	0.2 nTPM
Kidney	0.0 nTPM
Lung	0.0 nTPM
PBMC	0.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	3.4 nTPM
Rectum	6.5 nTPM
Small intestine	3.7 nTPM
Colon	0.0 nTPM

Plasma cells	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Respiratory ciliated cells	1.6 nTPM
Lung	2.9 nTPM
Bronchus	0.4 nTPM

Smooth muscle cells	10.1 nTPM
Prostate	19.4 nTPM
Skin	16.4 nTPM
Breast	16.4 nTPM
Adipose tissue	14.5 nTPM
Ovary	11.4 nTPM
Endometrium	8.8 nTPM
Heart muscle	8.7 nTPM
Skeletal muscle	5.3 nTPM
Pancreas	5.1 nTPM
Esophagus	4.6 nTPM
Bronchus	1.0 nTPM

T-cells	1.4 nTPM
Endometrium	12.8 nTPM
Prostate	4.7 nTPM
Skin	2.3 nTPM
Colon	1.0 nTPM
Liver	0.9 nTPM
Kidney	0.7 nTPM
Skeletal muscle	0.5 nTPM
Breast	0.2 nTPM
Adipose tissue	0.1 nTPM
Lung	0.0 nTPM
PBMC	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM

Astrocytes	48.0 nTPM
Brain	48.0 nTPM

Collecting duct cells	11.0 nTPM
Kidney	11.0 nTPM

Cone photoreceptor cells	4.2 nTPM
Eye	4.2 nTPM

Distal tubular cells	1.9 nTPM
Kidney	1.9 nTPM

Undifferentiated cells	5.7 nTPM
Rectum	10.2 nTPM
Colon	6.2 nTPM
Small intestine	0.8 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