Single cell type - LHX1 - The Human Protein Atlas

LHX1

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Pathway

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.	LHX1
Gene descriptionⁱ Full gene name according to HGNC.	LIM homeobox 1
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s).	Cancer-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.	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.	Horizontal & Bipolar cells - Neuronal signaling (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 (Horizontal cells, Collecting duct cells, Basal prostatic cells, Bipolar cells, Proximal tubular cells, Secretory cells)
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.	0.93
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 (Mammillary body, Upper rhombic lip, Cerebellar 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

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 (Horizontal cells, Collecting duct cells, Basal prostatic cells, Bipolar cells, Proximal tubular cells, Secretory cells)

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 (Mammillary body, Upper rhombic lip, Cerebellar 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

LHX1 is part of cluster 71 Horizontal & Bipolar cells - Neuronal signaling with confidenceⁱ 1
205 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.
PRR35	Proline rich 35	0.6912	71
AQP2	Aquaporin 2	0.6671	3
USP17L7	Ubiquitin specific peptidase 17 like family member 7	0.6616	71
SCRT2	Scratch family transcriptional repressor 2	0.6494	71
NAT16	N-acetyltransferase 16 (putative)	0.6463	71
C1QL1	Complement C1q like 1	0.6377	71
POU3F3	POU class 3 homeobox 3	0.6357	3
GJA10	Gap junction protein alpha 10	0.6304	71
JPH4	Junctophilin 4	0.6225	71
HOXB8	Homeobox B8	0.6167	3
EMX2	Empty spiracles homeobox 2	0.6165	3
ONECUT3	One cut homeobox 3	0.6158	71
PRDM13	PR/SET domain 13	0.6142	71
EDDM3A	Epididymal protein 3A	0.6051	3
TSC2	TSC complex subunit 2	0.6037	3

Adipocytes	0.1 nTPM
Breast	0.3 nTPM
Adipose tissue	0.0 nTPM

Alveolar cells type 1	0.0 nTPM
Lung	0.0 nTPM

Alveolar cells type 2	0.0 nTPM
Lung	0.0 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	0.4 nTPM
Kidney	5.2 nTPM
Spleen	0.4 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM

Ciliated cells	1.0 nTPM
Fallopian tube	3.5 nTPM
Endometrium	0.6 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM

Club cells	0.5 nTPM
Prostate	1.5 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM

Endothelial cells	0.3 nTPM
Prostate	5.1 nTPM
Fallopian tube	0.6 nTPM
Endometrium	0.2 nTPM
Testis	0.0 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Ovary	0.0 nTPM

Enteroendocrine cells	0.0 nTPM
Colon	0.1 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Fibroblasts	0.3 nTPM
Prostate	4.6 nTPM
Fallopian tube	0.2 nTPM
Pancreas	0.1 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM

Granulocytes	0.0 nTPM
Lung	0.0 nTPM
Tongue	0.0 nTPM
Fallopian tube	0.0 nTPM

Intestinal goblet cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Lymphatic endothelial cells	0.0 nTPM
Fallopian tube	0.1 nTPM
Ovary	0.0 nTPM

Macrophages	0.2 nTPM
Prostate	2.7 nTPM
Kidney	0.9 nTPM
Breast	0.4 nTPM
Fallopian tube	0.2 nTPM
Adipose tissue	0.1 nTPM
Salivary gland	0.1 nTPM
Vascular	0.1 nTPM
Testis	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM

Paneth cells	0.0 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM
Rectum	0.0 nTPM

Plasma cells	0.0 nTPM
Liver	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Fallopian tube	0.0 nTPM

Schwann cells	0.0 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Vascular	0.0 nTPM

Serous glandular cells	0.0 nTPM
Salivary gland	0.1 nTPM
Tongue	0.0 nTPM

Smooth muscle cells	0.4 nTPM
Prostate	4.9 nTPM
Fallopian tube	0.8 nTPM
Breast	0.5 nTPM
Adipose tissue	0.2 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Endometrium	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM
Ovary	0.0 nTPM

T-cells	0.1 nTPM
Prostate	0.9 nTPM
Stomach	0.4 nTPM
Tongue	0.4 nTPM
Breast	0.3 nTPM
Endometrium	0.1 nTPM
Adipose tissue	0.1 nTPM
Thymus	0.1 nTPM
Fallopian tube	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Vascular	0.0 nTPM

Undifferentiated cells	0.1 nTPM
Colon	0.1 nTPM
Small intestine	0.1 nTPM
Rectum	0.0 nTPM

Amygdala excitatory	0.3 nTPM
Amygdala	0.4 nTPM
Basal ganglia	0.4 nTPM
Hippocampus	0.4 nTPM
Cerebral cortex	0.3 nTPM
Hypothalamus	0.3 nTPM
Thalamus	0.0 nTPM

Astrocyte	0.3 nTPM
Hypothalamus	0.9 nTPM
Cerebellum	0.3 nTPM
Medulla oblongata	0.3 nTPM
Midbrain	0.3 nTPM
Pons	0.3 nTPM
Cerebral cortex	0.2 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Spinal cord	0.1 nTPM
Thalamus	0.1 nTPM
Hippocampus	0.0 nTPM

Bergmann glia	0.5 nTPM
Cerebellum	1.5 nTPM
Medulla oblongata	0.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	0.4 nTPM
Hypothalamus	1.8 nTPM
Cerebellum	0.7 nTPM
Medulla oblongata	0.7 nTPM
Pons	0.5 nTPM
Midbrain	0.3 nTPM
Spinal cord	0.3 nTPM
Thalamus	0.3 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM

Cerebellar inhibitory	54.2 nTPM
Cerebellum	70.9 nTPM
Midbrain	69.1 nTPM
Medulla oblongata	51.0 nTPM
Pons	47.0 nTPM
Spinal cord	33.0 nTPM

Cge interneuron	0.3 nTPM
Midbrain	0.5 nTPM
Basal ganglia	0.4 nTPM
Hypothalamus	0.3 nTPM
Thalamus	0.3 nTPM
Cerebral cortex	0.2 nTPM
Hippocampus	0.2 nTPM
Amygdala	0.1 nTPM

Choroid plexus epithelial cell	0.2 nTPM
Medulla oblongata	0.9 nTPM
Basal ganglia	0.0 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	1.9 nTPM
Cerebellum	7.9 nTPM
Pons	4.4 nTPM
Medulla oblongata	3.9 nTPM
Hypothalamus	2.7 nTPM
Thalamus	1.4 nTPM
Midbrain	0.8 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	0.3 nTPM
Midbrain	1.1 nTPM
Hypothalamus	0.3 nTPM
Amygdala	0.1 nTPM
Basal ganglia	0.1 nTPM
Cerebral cortex	0.1 nTPM
Hippocampus	0.1 nTPM

Deep-layer intratelencephalic	0.1 nTPM
Cerebral cortex	0.2 nTPM
Hypothalamus	0.2 nTPM
Amygdala	0.1 nTPM
Hippocampus	0.1 nTPM
Basal ganglia	0.0 nTPM

Deep-layer near-projecting	0.1 nTPM
Hypothalamus	0.2 nTPM
Basal ganglia	0.1 nTPM
Amygdala	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM

Eccentric medium spiny neuron	0.7 nTPM
Hippocampus	2.9 nTPM
Amygdala	0.4 nTPM
Hypothalamus	0.3 nTPM
Cerebral cortex	0.2 nTPM
Basal ganglia	0.1 nTPM
Thalamus	0.1 nTPM

Endothelial cell	0.6 nTPM
Cerebellum	3.9 nTPM
Midbrain	1.9 nTPM
Medulla oblongata	1.0 nTPM
Amygdala	0.0 nTPM
Basal ganglia	0.0 nTPM
Cerebral cortex	0.0 nTPM
Hippocampus	0.0 nTPM
Hypothalamus	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM
Thalamus	0.0 nTPM

Ependymal cell	1.3 nTPM
Hypothalamus	6.2 nTPM
Thalamus	2.0 nTPM
Basal ganglia	1.5 nTPM
Medulla oblongata	1.1 nTPM
Midbrain	0.6 nTPM
Hippocampus	0.3 nTPM
Amygdala	0.0 nTPM
Pons	0.0 nTPM
Spinal cord	0.0 nTPM