Single cell type - SHROOM1 - The Human Protein Atlas

SHROOM1

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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.	SHROOM1
Gene descriptionⁱ Full gene name according to HGNC.	Shroom family member 1
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.	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.	Enterocytes - Absorption (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.	Cell type enhanced (Distal enterocytes, Prostatic glandular cells, Hepatocytes, Proximal enterocytes)
Tau specificity scoreⁱ Tau specificity score is a numerical indicator of the specificity of the gene expression across cells or tissues. The value ranges from 0 and 1, where 0 indicates identical expression across all cells/tissue types, while 1 indicates expression in a single cell/tissue type.	0.58
Brain cluster specificityⁱ The RNA specificity category is based on mRNA expression levels in the analyzed cell cluster types based on snRNA-seq data from brain samples. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected. "cell type" refer to one of the 34 cluster names used to summarize the 2.5 million cells included in the brain cell representation.	Cell type enhanced (Endothelial cell, Oligodendrocyte)
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.	Not detected in immune cells
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); neXtProt protein existence (neXtProt evidence);and a Human Protein Atlas antibody- or RNA based score (HPA evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable.	Evidence at protein level

ASSAYSⁱ

SINGLE CELL TYPESⁱ A summary of normalized 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 RNA single cell type specificity: Cell type enhanced (Distal enterocytes, Prostatic glandular cells, Hepatocytes, Proximal enterocytes)

TISSUE CELL TYPEⁱ The tissue cell type section provides a cell type specificity prediction for all protein coding genes. More information on the data available can be found here and a description of the analysis here.
	Core cell typesⁱ The core cell type table displays data for a panel of eight cell types that are found in many tissues. Colored dots indicate that the selected gene has core cell type specificity in the indicated tissue. Grey dots indicate that cell type is present within that tissue, but the selected gene is not predicted to be enriched there. Category Alphabetical Enrichment Tissue specific cell typesⁱ This plot shows the enrichment score of the selected gene in all non-core cell types found within the profiled tissues, allowing comparisons between different cell types within different tissues. An enlarged symbol indicates classification of the gene as cell type enriched in the corresponding cell type.

SINGLE NUCLEI BRAINⁱ

Single nuclei cluster types

RNA brain cluster specificity: Cell type enhanced (Endothelial cell, Oligodendrocyte)

IMMUNE CELL TYPE EXPRESSION (RNA)ⁱ Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
HPA datasetⁱ The resulting transcript expression values calculated as nTPM, resulting from the internal normalization pipeline for 18 immune cell types and total peripheral blood mononuclear cells (PBMC). Lineage Expression Alphabetical Immune cell type specificity: Not detected in immune cells
Monaco datasetⁱ The transcript expression values (nTPM) resulting from the internal normalization pipeline are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al. Lineage Expression Alphabetical
Schmiedel datasetⁱ Transcript Per Million (TPM) values are visualized for 15 blood cell types from the Schmiedel et al. dataset. Lineage Expression Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

SINGLE CELL TYPE

SHROOM1 is part of cluster 5 Enterocytes - Absorption with confidenceⁱ 1
330 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell 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.	Clusterⁱ ID of the expression cluster of the neighboring gene.
TRPM4	Transient receptor potential cation channel subfamily M member 4	0.6987	5
MUC12	Mucin 12, cell surface associated	0.6760	5
SELENBP1	Selenium binding protein 1	0.6682	5
UGT2B17	UDP glucuronosyltransferase family 2 member B17	0.6590	5
SULT1A4	Sulfotransferase family 1A member 4	0.6499	5
SLC26A2	Solute carrier family 26 member 2	0.6436	5
TST	Thiosulfate sulfurtransferase	0.6405	5
FABP1	Fatty acid binding protein 1	0.6405	5
CLDN23	Claudin 23	0.6401	5
CLCN2	Chloride voltage-gated channel 2	0.6391	5
HSD11B2	Hydroxysteroid 11-beta dehydrogenase 2	0.6324	5
CA2	Carbonic anhydrase 2	0.6190	5
MMP15	Matrix metallopeptidase 15	0.6163	5
OR9Q2	Olfactory receptor family 9 subfamily Q member 2	0.6131	5
BNIP5	BCL2 interacting protein 5	0.6121	5

Adipocytes	17.8 nTPM
Adipose tissue	22.9 nTPM
Breast	12.6 nTPM

Alveolar cells type 1	5.4 nTPM
Lung	5.4 nTPM

Alveolar cells type 2	19.6 nTPM
Lung	19.6 nTPM

Astrocytes	18.0 nTPM
Brain	18.0 nTPM

B-cells	1.2 nTPM
Lung	4.0 nTPM
Adipose tissue	2.9 nTPM
Salivary gland	2.2 nTPM
Thymus	1.6 nTPM
PBMC	1.5 nTPM
Bone marrow	1.4 nTPM
Stomach	1.3 nTPM
Spleen	0.7 nTPM
Lymph node	0.5 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Skin	0.0 nTPM
Esophagus	0.0 nTPM

Ciliated cells	4.3 nTPM
Endometrium	6.8 nTPM
Bronchus	5.6 nTPM
Fallopian tube	2.9 nTPM
Lung	1.8 nTPM

Club cells	31.9 nTPM
Prostate	88.0 nTPM
Bronchus	4.7 nTPM
Lung	3.1 nTPM

Endothelial cells	19.9 nTPM
Placenta	52.2 nTPM
Prostate	36.2 nTPM
Ovary	32.6 nTPM
Endometrium	30.7 nTPM
Thymus	30.2 nTPM
Testis	22.3 nTPM
Vascular	20.0 nTPM
Fallopian tube	19.5 nTPM
Lung	19.1 nTPM
Liver	18.9 nTPM
Salivary gland	14.1 nTPM
Skeletal muscle	12.8 nTPM
Tongue	12.2 nTPM
Esophagus	10.4 nTPM
Heart muscle	8.6 nTPM
Pancreas	7.8 nTPM
Breast	5.3 nTPM
Skin	4.8 nTPM

Enteroendocrine cells	21.2 nTPM
Rectum	25.2 nTPM
Colon	24.8 nTPM
Small intestine	13.7 nTPM

Fibroblasts	5.5 nTPM
Prostate	16.5 nTPM
Esophagus	7.6 nTPM
Thymus	5.8 nTPM
Pancreas	5.7 nTPM
Breast	5.7 nTPM
Adipose tissue	5.5 nTPM
Skeletal muscle	5.1 nTPM
Lung	5.0 nTPM
Fallopian tube	4.8 nTPM
Liver	4.7 nTPM
Salivary gland	4.5 nTPM
Stomach	4.3 nTPM
Placenta	4.2 nTPM
Vascular	3.3 nTPM
Skin	2.9 nTPM
Heart muscle	2.0 nTPM

Granulocytes	5.5 nTPM
Lung	7.6 nTPM
Tongue	4.9 nTPM
Fallopian tube	4.2 nTPM

Intestinal goblet cells	27.3 nTPM
Small intestine	38.9 nTPM
Rectum	23.4 nTPM
Colon	19.7 nTPM

Lymphatic endothelial cells	5.4 nTPM
Ovary	5.5 nTPM
Fallopian tube	5.3 nTPM

Macrophages	4.7 nTPM
Kidney	12.4 nTPM
Vascular	10.5 nTPM
Thymus	8.4 nTPM
Stomach	7.7 nTPM
Prostate	7.3 nTPM
Adipose tissue	6.8 nTPM
Skeletal muscle	6.7 nTPM
Endometrium	5.5 nTPM
Fallopian tube	4.4 nTPM
Tongue	3.3 nTPM
Salivary gland	3.2 nTPM
Lung	3.1 nTPM
Bone marrow	3.0 nTPM
Spleen	2.0 nTPM
Testis	1.9 nTPM
Esophagus	1.3 nTPM
Skin	1.1 nTPM
Breast	0.7 nTPM
Pancreas	0.0 nTPM

Paneth cells	41.2 nTPM
Colon	50.7 nTPM
Small intestine	44.9 nTPM
Rectum	27.9 nTPM

Basal prostatic cells	45.8 nTPM
Prostate	45.8 nTPM

Cholangiocytes	32.4 nTPM
Liver	32.4 nTPM

Collecting duct cells	11.7 nTPM
Kidney	11.7 nTPM

Cytotrophoblasts	6.9 nTPM
Placenta	6.9 nTPM

Plasma cells	3.5 nTPM
Salivary gland	8.1 nTPM
Liver	8.0 nTPM
Fallopian tube	5.5 nTPM
Stomach	3.8 nTPM
Thymus	2.3 nTPM
Spleen	0.5 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Schwann cells	12.8 nTPM
Esophagus	24.0 nTPM
Vascular	10.4 nTPM
Adipose tissue	3.9 nTPM

Serous glandular cells	6.0 nTPM
Tongue	8.8 nTPM
Salivary gland	3.1 nTPM

Smooth muscle cells	6.8 nTPM
Liver	24.6 nTPM
Prostate	14.0 nTPM
Lung	8.2 nTPM
Adipose tissue	8.0 nTPM
Tongue	7.5 nTPM
Skeletal muscle	7.4 nTPM
Breast	6.1 nTPM
Ovary	6.0 nTPM
Placenta	5.5 nTPM
Endometrium	5.2 nTPM
Thymus	3.5 nTPM
Fallopian tube	3.5 nTPM
Skin	3.1 nTPM
Salivary gland	3.1 nTPM
Vascular	2.5 nTPM
Esophagus	1.2 nTPM

T-cells	2.3 nTPM
Prostate	9.0 nTPM
Vascular	5.6 nTPM
Endometrium	4.3 nTPM
Skin	3.9 nTPM
PBMC	3.8 nTPM
Lung	3.2 nTPM
Liver	3.0 nTPM
Adipose tissue	3.0 nTPM
Colon	2.9 nTPM
Salivary gland	1.9 nTPM
Tongue	1.8 nTPM
Breast	1.3 nTPM
Kidney	0.9 nTPM
Thymus	0.9 nTPM
Fallopian tube	0.9 nTPM
Skeletal muscle	0.4 nTPM
Stomach	0.4 nTPM
Lymph node	0.2 nTPM
Bone marrow	0.1 nTPM
Esophagus	0.0 nTPM
Spleen	0.0 nTPM

Undifferentiated cells	20.9 nTPM
Small intestine	25.1 nTPM
Rectum	22.1 nTPM
Colon	15.4 nTPM

Amygdala excitatory	3.8 nTPM
Cerebral cortex	5.3 nTPM
Amygdala	5.1 nTPM
Hippocampus	4.9 nTPM
Basal ganglia	3.3 nTPM
Hypothalamus	2.2 nTPM
Thalamus	1.8 nTPM

Astrocyte	19.3 nTPM
Hippocampus	30.9 nTPM
Cerebral cortex	28.9 nTPM
Amygdala	21.2 nTPM
Pons	20.9 nTPM
Cerebellum	19.9 nTPM
Midbrain	17.7 nTPM
Basal ganglia	17.5 nTPM
Medulla oblongata	14.9 nTPM
Spinal cord	14.3 nTPM
Hypothalamus	13.4 nTPM
Thalamus	12.9 nTPM

Bergmann glia	24.6 nTPM
Medulla oblongata	27.7 nTPM
Pons	24.5 nTPM
Cerebellum	21.7 nTPM

Central nervous system macrophage	3.3 nTPM
Spinal cord	5.6 nTPM
Hippocampus	5.0 nTPM
Pons	4.0 nTPM
Midbrain	3.8 nTPM
Cerebral cortex	3.5 nTPM
Cerebellum	2.8 nTPM
Thalamus	2.6 nTPM
Hypothalamus	2.5 nTPM
Medulla oblongata	2.4 nTPM
Amygdala	2.0 nTPM
Basal ganglia	1.9 nTPM

Cerebellar inhibitory	6.4 nTPM
Cerebellum	7.7 nTPM
Midbrain	7.5 nTPM
Pons	7.2 nTPM
Medulla oblongata	6.8 nTPM
Spinal cord	2.7 nTPM

Cge interneuron	2.5 nTPM
Basal ganglia	3.4 nTPM
Hypothalamus	3.4 nTPM
Amygdala	2.4 nTPM
Hippocampus	2.4 nTPM
Cerebral cortex	2.3 nTPM
Midbrain	2.0 nTPM
Thalamus	1.7 nTPM

Choroid plexus epithelial cell	6.7 nTPM
Hippocampus	8.3 nTPM
Medulla oblongata	6.7 nTPM
Basal ganglia	6.3 nTPM
Thalamus	5.5 nTPM

Committed oligodendrocyte precursor	17.2 nTPM
Hypothalamus	48.5 nTPM
Thalamus	27.2 nTPM
Basal ganglia	23.5 nTPM
Amygdala	20.9 nTPM
Cerebral cortex	14.6 nTPM
Pons	11.5 nTPM
Cerebellum	11.1 nTPM
Medulla oblongata	10.3 nTPM
Hippocampus	9.6 nTPM
Spinal cord	7.4 nTPM
Midbrain	4.2 nTPM

Deep-layer corticothalamic and 6b	2.9 nTPM
Hippocampus	3.7 nTPM
Basal ganglia	3.2 nTPM
Amygdala	2.9 nTPM
Cerebral cortex	2.6 nTPM
Hypothalamus	2.5 nTPM
Midbrain	2.2 nTPM

Deep-layer intratelencephalic	3.9 nTPM
Cerebral cortex	4.3 nTPM
Hippocampus	4.3 nTPM
Basal ganglia	4.2 nTPM
Hypothalamus	3.6 nTPM
Amygdala	2.9 nTPM

Deep-layer near-projecting	4.5 nTPM
Hippocampus	7.2 nTPM
Basal ganglia	4.8 nTPM
Cerebral cortex	4.5 nTPM
Amygdala	3.0 nTPM
Hypothalamus	3.0 nTPM

Eccentric medium spiny neuron	5.2 nTPM
Amygdala	6.2 nTPM
Cerebral cortex	6.1 nTPM
Hypothalamus	5.5 nTPM
Basal ganglia	4.8 nTPM
Hippocampus	4.6 nTPM
Thalamus	4.3 nTPM

Endothelial cell	112.2 nTPM
Hippocampus	151.3 nTPM
Cerebral cortex	143.2 nTPM
Spinal cord	127.7 nTPM
Amygdala	125.2 nTPM
Cerebellum	120.0 nTPM
Pons	115.5 nTPM
Midbrain	99.2 nTPM
Thalamus	96.6 nTPM
Medulla oblongata	91.3 nTPM
Basal ganglia	84.8 nTPM
Hypothalamus	79.4 nTPM

Ependymal cell	4.8 nTPM
Medulla oblongata	6.4 nTPM
Amygdala	6.3 nTPM
Spinal cord	5.7 nTPM
Hypothalamus	5.4 nTPM
Midbrain	4.4 nTPM
Basal ganglia	4.1 nTPM
Thalamus	4.0 nTPM
Hippocampus	3.9 nTPM
Pons	2.7 nTPM