Single cell type - IGFL4 - The Human Protein Atlas

IGFL4

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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.	IGFL4
Gene descriptionⁱ Full gene name according to HGNC.	IGF like family member 4
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.	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.	Photoreceptor cells - Visual perception (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 (Rod photoreceptor cells, Cone photoreceptor cells, Inhibitory neurons, Excitatory neurons, Bipolar 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.	0.92
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.	Low cell type specificity
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.	Low immune cell specificity
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 transcript 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 (Rod photoreceptor cells, Cone photoreceptor cells, Inhibitory neurons, Excitatory neurons, Bipolar 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: Low cell type specificity

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: Low immune cell specificity
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

IGFL4 is part of cluster 66 Photoreceptor cells - Visual perception with confidenceⁱ 1
340 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.
PDE6A	Phosphodiesterase 6A	0.8469	66
KCNJ14	Potassium inwardly rectifying channel subfamily J member 14	0.8451	66
CNGB1	Cyclic nucleotide gated channel subunit beta 1	0.8437	66
PDE6B	Phosphodiesterase 6B	0.8395	66
KCNB1	Potassium voltage-gated channel subfamily B member 1	0.8368	66
SAG	S-antigen visual arrestin	0.8340	66
PRPH2	Peripherin 2	0.8288	66
RP1	RP1 axonemal microtubule associated	0.8275	66
ABCA4	ATP binding cassette subfamily A member 4	0.8258	66
CNGA1	Cyclic nucleotide gated channel subunit alpha 1	0.8213	66
UBE2QL1	Ubiquitin conjugating enzyme E2 Q family like 1	0.8211	66
GNAT1	G protein subunit alpha transducin 1	0.8199	66
GAL3ST3	Galactose-3-O-sulfotransferase 3	0.8164	66
CLUL1	Clusterin like 1	0.8112	66
NRL	Neural retina leucine zipper	0.8097	66

IMMUNE CELLS

IGFL4 is part of cluster 20 Non-specific - DNA binding with confidenceⁱ 0.89
266 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.
BRD4	Bromodomain containing 4	0.9762	20
TCEANC2	Transcription elongation factor A N-terminal and central domain containing 2	0.9762	20
USF3	Upstream transcription factor family member 3	0.9762	20
EPC1	Enhancer of polycomb homolog 1	0.9286	21
ZNF70	Zinc finger protein 70	0.9286	20
RNPC3	RNA binding region (RNP1, RRM) containing 3	0.9286	21
TRIM72	Tripartite motif containing 72	0.9286	20
GVQW3	GVQW motif containing 3	0.9286	20
FAM240B	Family with sequence similarity 240 member B	0.9048	20
CCDC194	Coiled-coil domain containing 194	0.9048	20
TINCR	TINCR ubiquitin domain containing	0.9048	20
SCRG1	Stimulator of chondrogenesis 1	0.9048	20
SRRM2	Serine/arginine repetitive matrix 2	0.9048	21
LENG8	Leukocyte receptor cluster member 8	0.8810	20
KIN	Kin17 DNA and RNA binding protein	0.8810	20

Adipocytes	0.0 nTPM
Adipose tissue	0.0 nTPM
Breast	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	2.5 nTPM
Brain	2.5 nTPM

B-cells	0.0 nTPM
Kidney	0.0 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
Spleen	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM

Ciliated cells	0.0 nTPM
Endometrium	0.0 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM
Fallopian tube	0.0 nTPM

Club cells	0.0 nTPM
Bronchus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM

Endothelial cells	0.0 nTPM
Testis	0.3 nTPM
Thymus	0.1 nTPM
Heart muscle	0.0 nTPM
Liver	0.0 nTPM
Placenta	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Tongue	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM
Ovary	0.0 nTPM

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

Fibroblasts	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
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Stomach	0.0 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	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	0.0 nTPM
Ovary	0.0 nTPM

Macrophages	0.0 nTPM
Testis	0.6 nTPM
Tongue	0.2 nTPM
Kidney	0.0 nTPM
Endometrium	0.0 nTPM
Pancreas	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	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
Lung	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

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

Basal keratinocytes	1.1 nTPM
Skin	1.2 nTPM
Tongue	1.0 nTPM

Basal respiratory cells	0.8 nTPM
Bronchus	0.8 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	0.0 nTPM
Tongue	0.0 nTPM

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

T-cells	0.0 nTPM
Tongue	0.1 nTPM
Colon	0.0 nTPM
Kidney	0.0 nTPM
Liver	0.0 nTPM
Endometrium	0.0 nTPM
PBMC	0.0 nTPM
Skin	0.0 nTPM
Skeletal muscle	0.0 nTPM
Adipose tissue	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
Lung	0.0 nTPM
Prostate	0.0 nTPM
Salivary gland	0.0 nTPM
Thymus	0.0 nTPM
Vascular	0.0 nTPM
Breast	0.0 nTPM
Fallopian tube	0.0 nTPM

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

Amygdala excitatory	52.2 nTPM
Hypothalamus	79.6 nTPM
Hippocampus	56.0 nTPM
Amygdala	50.5 nTPM
Basal ganglia	47.4 nTPM
Cerebral cortex	46.4 nTPM
Thalamus	33.1 nTPM

Astrocyte	9.8 nTPM
Amygdala	18.2 nTPM
Cerebral cortex	16.9 nTPM
Hippocampus	14.2 nTPM
Basal ganglia	11.5 nTPM
Thalamus	9.9 nTPM
Hypothalamus	9.8 nTPM
Midbrain	6.7 nTPM
Medulla oblongata	5.9 nTPM
Pons	5.5 nTPM
Spinal cord	5.0 nTPM
Cerebellum	4.7 nTPM

Bergmann glia	15.1 nTPM
Pons	23.0 nTPM
Cerebellum	11.7 nTPM
Medulla oblongata	10.7 nTPM

Central nervous system macrophage	0.8 nTPM
Cerebral cortex	1.9 nTPM
Amygdala	1.3 nTPM
Hippocampus	1.0 nTPM
Hypothalamus	1.0 nTPM
Thalamus	0.7 nTPM
Basal ganglia	0.6 nTPM
Spinal cord	0.6 nTPM
Pons	0.5 nTPM
Cerebellum	0.4 nTPM
Midbrain	0.4 nTPM
Medulla oblongata	0.1 nTPM

Cerebellar inhibitory	11.3 nTPM
Medulla oblongata	13.6 nTPM
Midbrain	11.5 nTPM
Pons	11.5 nTPM
Spinal cord	11.0 nTPM
Cerebellum	8.9 nTPM

Cge interneuron	52.3 nTPM
Hypothalamus	64.6 nTPM
Amygdala	55.7 nTPM
Cerebral cortex	54.3 nTPM
Hippocampus	50.2 nTPM
Basal ganglia	49.2 nTPM
Thalamus	46.7 nTPM
Midbrain	45.1 nTPM

Choroid plexus epithelial cell	0.1 nTPM
Medulla oblongata	0.4 nTPM
Basal ganglia	0.1 nTPM
Hippocampus	0.0 nTPM
Thalamus	0.0 nTPM

Committed oligodendrocyte precursor	12.0 nTPM
Spinal cord	22.1 nTPM
Amygdala	15.2 nTPM
Cerebral cortex	12.7 nTPM
Basal ganglia	12.6 nTPM
Midbrain	12.6 nTPM
Hypothalamus	12.3 nTPM
Thalamus	11.5 nTPM
Pons	10.6 nTPM
Medulla oblongata	9.0 nTPM
Hippocampus	8.5 nTPM
Cerebellum	4.8 nTPM

Deep-layer corticothalamic and 6b	64.8 nTPM
Hypothalamus	76.4 nTPM
Amygdala	68.7 nTPM
Cerebral cortex	62.8 nTPM
Hippocampus	61.8 nTPM
Basal ganglia	60.4 nTPM
Midbrain	58.8 nTPM

Deep-layer intratelencephalic	47.6 nTPM
Hypothalamus	54.2 nTPM
Hippocampus	53.6 nTPM
Amygdala	52.0 nTPM
Cerebral cortex	42.8 nTPM
Basal ganglia	35.5 nTPM

Deep-layer near-projecting	67.6 nTPM
Hypothalamus	79.2 nTPM
Amygdala	68.2 nTPM
Basal ganglia	67.2 nTPM
Cerebral cortex	63.8 nTPM
Hippocampus	59.5 nTPM

Eccentric medium spiny neuron	45.4 nTPM
Amygdala	52.3 nTPM
Hippocampus	51.4 nTPM
Cerebral cortex	50.1 nTPM
Hypothalamus	47.1 nTPM
Basal ganglia	35.9 nTPM
Thalamus	35.3 nTPM

Endothelial cell	0.8 nTPM
Amygdala	2.2 nTPM
Spinal cord	1.7 nTPM
Hypothalamus	1.2 nTPM
Medulla oblongata	1.0 nTPM
Midbrain	0.9 nTPM
Cerebral cortex	0.6 nTPM
Hippocampus	0.6 nTPM
Pons	0.6 nTPM
Basal ganglia	0.0 nTPM
Cerebellum	0.0 nTPM
Thalamus	0.0 nTPM

Ependymal cell	1.9 nTPM
Medulla oblongata	3.5 nTPM
Amygdala	2.8 nTPM
Hypothalamus	2.7 nTPM
Pons	2.4 nTPM
Hippocampus	2.2 nTPM
Thalamus	1.6 nTPM
Midbrain	1.3 nTPM
Basal ganglia	0.9 nTPM
Spinal cord	0.0 nTPM