Single cell type - LAMB1 - The Human Protein Atlas

LAMB1

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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.	LAMB1
Gene descriptionⁱ Full gene name according to HGNC.	Laminin subunit beta 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-related genes Disease related genes Human disease related genes 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.	Secreted, Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	9

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.	Fibroblasts - ECM organization (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 (Endometrial stromal cells, Mesothelial cells, Peritubular cells, Fibroblasts)
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.	0.53
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 (Choroid plexus epithelial cell, Midbrain-derived inhibitory)
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
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.	Protein predicted to be secreted

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 (Endometrial stromal cells, Mesothelial cells, Peritubular cells, Fibroblasts)

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 (Choroid plexus epithelial cell, Midbrain-derived inhibitory)

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

LAMB1 is part of cluster 53 Fibroblasts - ECM organization with confidenceⁱ 1
305 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.
NID1	Nidogen 1	0.7771	9
FGF10	Fibroblast growth factor 10	0.7571	53
LAMC1	Laminin subunit gamma 1	0.6543	53
LAMA2	Laminin subunit alpha 2	0.6542	53
PCDH18	Protocadherin 18	0.6527	53
TIMP3	TIMP metallopeptidase inhibitor 3	0.6394	53
COL4A2	Collagen type IV alpha 2 chain	0.6218	48
COL4A1	Collagen type IV alpha 1 chain	0.6097	48
COL6A3	Collagen type VI alpha 3 chain	0.6081	53
CD248	CD248 molecule	0.6000	53
PCDHB16	Protocadherin beta 16	0.5894	53
IGF1	Insulin like growth factor 1	0.5893	9
S1PR3	Sphingosine-1-phosphate receptor 3	0.5864	48
PCDHGA5	Protocadherin gamma subfamily A, 5	0.5839	9
APOD	Apolipoprotein D	0.5623	53

Adipocytes	90.2 nTPM
Adipose tissue	127.9 nTPM
Breast	52.6 nTPM

Alveolar cells type 1	3.8 nTPM
Lung	3.8 nTPM

Alveolar cells type 2	0.8 nTPM
Lung	0.8 nTPM

Astrocytes	2.8 nTPM
Brain	2.8 nTPM

B-cells	3.2 nTPM
Thymus	12.8 nTPM
PBMC	10.8 nTPM
Salivary gland	6.3 nTPM
Skin	5.1 nTPM
Adipose tissue	3.3 nTPM
Bone marrow	2.1 nTPM
Lymph node	0.4 nTPM
Spleen	0.4 nTPM
Stomach	0.4 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM

Ciliated cells	8.9 nTPM
Endometrium	27.0 nTPM
Fallopian tube	3.0 nTPM
Lung	2.9 nTPM
Bronchus	2.6 nTPM

Club cells	6.2 nTPM
Prostate	7.5 nTPM
Lung	5.6 nTPM
Bronchus	5.5 nTPM

Endothelial cells	49.2 nTPM
Heart muscle	143.1 nTPM
Salivary gland	87.0 nTPM
Skeletal muscle	86.5 nTPM
Endometrium	86.3 nTPM
Vascular	85.2 nTPM
Pancreas	72.4 nTPM
Thymus	53.0 nTPM
Tongue	48.8 nTPM
Breast	36.0 nTPM
Placenta	31.2 nTPM
Ovary	29.5 nTPM
Lung	26.4 nTPM
Esophagus	20.3 nTPM
Fallopian tube	18.9 nTPM
Testis	18.0 nTPM
Prostate	17.6 nTPM
Skin	13.8 nTPM
Liver	11.3 nTPM

Enteroendocrine cells	17.0 nTPM
Rectum	28.5 nTPM
Colon	15.5 nTPM
Small intestine	6.9 nTPM

Fibroblasts	156.5 nTPM
Salivary gland	524.4 nTPM
Heart muscle	370.8 nTPM
Vascular	321.7 nTPM
Thymus	298.1 nTPM
Lung	241.4 nTPM
Skeletal muscle	189.9 nTPM
Breast	124.6 nTPM
Adipose tissue	97.1 nTPM
Pancreas	59.9 nTPM
Placenta	58.8 nTPM
Stomach	53.3 nTPM
Fallopian tube	48.7 nTPM
Prostate	48.2 nTPM
Esophagus	45.1 nTPM
Skin	15.4 nTPM
Liver	7.1 nTPM

Granulocytes	0.8 nTPM
Fallopian tube	1.5 nTPM
Lung	1.0 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	8.7 nTPM
Rectum	14.8 nTPM
Colon	7.9 nTPM
Small intestine	3.5 nTPM

Lymphatic endothelial cells	66.5 nTPM
Ovary	87.3 nTPM
Fallopian tube	45.8 nTPM

Macrophages	4.4 nTPM
Vascular	13.7 nTPM
Endometrium	12.9 nTPM
Thymus	12.2 nTPM
Skeletal muscle	11.7 nTPM
Fallopian tube	4.6 nTPM
Tongue	3.3 nTPM
Salivary gland	3.2 nTPM
Lung	2.8 nTPM
Kidney	2.7 nTPM
Esophagus	2.6 nTPM
Breast	2.6 nTPM
Prostate	2.4 nTPM
Pancreas	2.1 nTPM
Spleen	2.0 nTPM
Testis	1.9 nTPM
Skin	1.1 nTPM
Adipose tissue	1.1 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	20.3 nTPM
Rectum	32.3 nTPM
Colon	18.1 nTPM
Small intestine	10.4 nTPM

Basal keratinocytes	13.4 nTPM
Skin	13.4 nTPM
Tongue	13.3 nTPM

Basal prostatic cells	14.3 nTPM
Prostate	14.3 nTPM

Basal respiratory cells	19.2 nTPM
Bronchus	19.2 nTPM

Bipolar cells	19.9 nTPM
Eye	19.9 nTPM

Plasma cells	3.8 nTPM
Thymus	9.7 nTPM
Salivary gland	9.4 nTPM
Liver	5.0 nTPM
Fallopian tube	4.8 nTPM
Spleen	0.7 nTPM
Stomach	0.4 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM

Schwann cells	105.1 nTPM
Vascular	243.4 nTPM
Esophagus	71.9 nTPM
Adipose tissue	0.0 nTPM

Serous glandular cells	41.7 nTPM
Salivary gland	79.1 nTPM
Tongue	4.4 nTPM

Smooth muscle cells	89.5 nTPM
Lung	301.0 nTPM
Tongue	249.1 nTPM
Adipose tissue	181.5 nTPM
Endometrium	162.3 nTPM
Placenta	117.2 nTPM
Vascular	95.5 nTPM
Skeletal muscle	92.4 nTPM
Thymus	77.3 nTPM
Salivary gland	54.5 nTPM
Ovary	28.0 nTPM
Liver	23.3 nTPM
Breast	16.4 nTPM
Prostate	14.0 nTPM
Fallopian tube	7.7 nTPM
Skin	6.4 nTPM
Esophagus	6.0 nTPM

T-cells	4.7 nTPM
Endometrium	20.5 nTPM
PBMC	11.9 nTPM
Vascular	11.3 nTPM
Salivary gland	8.2 nTPM
Tongue	6.0 nTPM
Kidney	5.3 nTPM
Skeletal muscle	4.5 nTPM
Thymus	4.3 nTPM
Skin	3.5 nTPM
Prostate	3.2 nTPM
Colon	2.9 nTPM
Fallopian tube	2.7 nTPM
Adipose tissue	2.6 nTPM
Breast	2.6 nTPM
Esophagus	2.4 nTPM
Lung	2.4 nTPM
Liver	2.3 nTPM
Bone marrow	1.1 nTPM
Lymph node	0.7 nTPM
Stomach	0.5 nTPM
Spleen	0.0 nTPM

Undifferentiated cells	23.0 nTPM
Rectum	34.3 nTPM
Small intestine	22.3 nTPM
Colon	12.5 nTPM

Amygdala excitatory	87.7 nTPM
Amygdala	127.8 nTPM
Cerebral cortex	103.4 nTPM
Hippocampus	94.5 nTPM
Hypothalamus	89.9 nTPM
Basal ganglia	64.7 nTPM
Thalamus	45.8 nTPM

Astrocyte	6.2 nTPM
Thalamus	10.0 nTPM
Basal ganglia	7.8 nTPM
Cerebral cortex	7.7 nTPM
Hypothalamus	7.7 nTPM
Medulla oblongata	6.2 nTPM
Amygdala	6.1 nTPM
Hippocampus	6.1 nTPM
Midbrain	5.3 nTPM
Pons	5.2 nTPM
Spinal cord	3.3 nTPM
Cerebellum	2.8 nTPM

Bergmann glia	7.4 nTPM
Pons	10.1 nTPM
Cerebellum	7.9 nTPM
Medulla oblongata	4.3 nTPM

Central nervous system macrophage	5.7 nTPM
Thalamus	11.5 nTPM
Hypothalamus	9.1 nTPM
Medulla oblongata	7.3 nTPM
Basal ganglia	5.5 nTPM
Pons	5.0 nTPM
Cerebral cortex	4.9 nTPM
Amygdala	4.3 nTPM
Cerebellum	3.8 nTPM
Spinal cord	3.8 nTPM
Hippocampus	3.4 nTPM
Midbrain	3.4 nTPM

Cerebellar inhibitory	73.3 nTPM
Medulla oblongata	86.5 nTPM
Cerebellum	80.7 nTPM
Spinal cord	71.5 nTPM
Midbrain	66.6 nTPM
Pons	61.4 nTPM

Cge interneuron	18.0 nTPM
Hippocampus	27.3 nTPM
Thalamus	20.5 nTPM
Midbrain	19.5 nTPM
Cerebral cortex	18.1 nTPM
Basal ganglia	15.7 nTPM
Amygdala	15.1 nTPM
Hypothalamus	9.9 nTPM

Choroid plexus epithelial cell	324.0 nTPM
Medulla oblongata	434.2 nTPM
Basal ganglia	373.9 nTPM
Thalamus	246.6 nTPM
Hippocampus	241.3 nTPM

Committed oligodendrocyte precursor	31.5 nTPM
Medulla oblongata	63.3 nTPM
Cerebellum	47.6 nTPM
Thalamus	40.7 nTPM
Basal ganglia	39.4 nTPM
Pons	37.2 nTPM
Hippocampus	32.3 nTPM
Spinal cord	22.1 nTPM
Cerebral cortex	19.6 nTPM
Amygdala	19.2 nTPM
Hypothalamus	15.0 nTPM
Midbrain	10.1 nTPM

Deep-layer corticothalamic and 6b	14.4 nTPM
Hippocampus	20.0 nTPM
Midbrain	16.6 nTPM
Cerebral cortex	15.3 nTPM
Basal ganglia	15.0 nTPM
Amygdala	14.1 nTPM
Hypothalamus	5.3 nTPM

Deep-layer intratelencephalic	48.8 nTPM
Amygdala	56.9 nTPM
Hippocampus	53.7 nTPM
Cerebral cortex	52.5 nTPM
Basal ganglia	42.2 nTPM
Hypothalamus	38.7 nTPM

Deep-layer near-projecting	14.9 nTPM
Hippocampus	24.1 nTPM
Cerebral cortex	18.0 nTPM
Basal ganglia	16.5 nTPM
Amygdala	12.8 nTPM
Hypothalamus	2.8 nTPM

Eccentric medium spiny neuron	50.5 nTPM
Cerebral cortex	64.3 nTPM
Amygdala	61.1 nTPM
Hypothalamus	52.2 nTPM
Thalamus	47.6 nTPM
Basal ganglia	44.5 nTPM
Hippocampus	33.6 nTPM

Endothelial cell	13.4 nTPM
Hypothalamus	31.0 nTPM
Medulla oblongata	19.5 nTPM
Basal ganglia	16.8 nTPM
Cerebral cortex	16.6 nTPM
Amygdala	15.6 nTPM
Pons	12.5 nTPM
Cerebellum	11.6 nTPM
Hippocampus	9.6 nTPM
Thalamus	6.8 nTPM
Spinal cord	5.2 nTPM
Midbrain	1.9 nTPM

Ependymal cell	10.5 nTPM
Hypothalamus	20.5 nTPM
Medulla oblongata	12.3 nTPM
Thalamus	11.7 nTPM
Spinal cord	11.5 nTPM
Basal ganglia	11.0 nTPM
Midbrain	9.5 nTPM
Amygdala	8.0 nTPM
Pons	5.5 nTPM
Hippocampus	4.9 nTPM