Single cell type - TTC9 - The Human Protein Atlas

TTC9

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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.	TTC9
Gene descriptionⁱ Full gene name according to HGNC.	Tetratricopeptide repeat domain 9
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.	1

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.	Suprabasal keratinocytes - Cornification (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 (Ionocytes, Ciliated 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.	0.55
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 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 (Ionocytes, Ciliated 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

TTC9 is part of cluster 59 Suprabasal keratinocytes - Cornification with confidenceⁱ 1
186 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.
PLEKHN1	Pleckstrin homology domain containing N1	0.6336	59
TRIM16	Tripartite motif containing 16	0.6230	35
PGLYRP4	Peptidoglycan recognition protein 4	0.6051	35
CST6	Cystatin E/M	0.6021	45
SERPINB11	Serpin family B member 11	0.5853	59
RHOD	Ras homolog family member D	0.5815	45
RAET1G	Retinoic acid early transcript 1G	0.5803	59
LCE3D	Late cornified envelope 3D	0.5764	59
CSTB	Cystatin B	0.5763	59
ENSG00000251537	Novel tripartite motif-containing 16 (TRIM16) and CMT1A duplicated region transcript 1 (CDRT1) protein	0.5761	35
RNF39	Ring finger protein 39	0.5704	35
TMPRSS11E	Transmembrane serine protease 11E	0.5680	59
EPGN	Epithelial mitogen	0.5644	59
TGM1	Transglutaminase 1	0.5518	59
ADGRF1	Adhesion G protein-coupled receptor F1	0.5507	35

IMMUNE CELLS

TTC9 is part of cluster 21 Neutrophils - Unknown function with confidenceⁱ 0.98
492 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.
PRKD2	Protein kinase D2	0.9762	21
TIGD1	Tigger transposable element derived 1	0.9524	21
METTL4	Methyltransferase 4, N6-adenosine	0.9286	21
UMAD1	UBAP1-MVB12-associated (UMA) domain containing 1	0.9286	21
ZNF850	Zinc finger protein 850	0.9048	43
CBX7	Chromobox 7	0.9048	21
MYL9	Myosin light chain 9	0.9048	21
DNAI7	Dynein axonemal intermediate chain 7	0.9048	24
ZNF737	Zinc finger protein 737	0.9048	43
HELZ2	Helicase with zinc finger 2	0.9048	21
RFX3	Regulatory factor X3	0.9048	21
ABCG1	ATP binding cassette subfamily G member 1	0.9048	21
RYK	Receptor like tyrosine kinase	0.9048	21
MBLAC1	Metallo-beta-lactamase domain containing 1	0.9048	21
PRELID3A	PRELI domain containing 3A	0.8810	21

Adipocytes	3.6 nTPM
Breast	5.8 nTPM
Adipose tissue	1.4 nTPM

Alveolar cells type 1	11.8 nTPM
Lung	11.8 nTPM

Alveolar cells type 2	12.6 nTPM
Lung	12.6 nTPM

Astrocytes	1.2 nTPM
Brain	1.2 nTPM

B-cells	14.6 nTPM
PBMC	35.4 nTPM
Lung	26.8 nTPM
Salivary gland	25.5 nTPM
Thymus	23.0 nTPM
Liver	14.5 nTPM
Adipose tissue	14.4 nTPM
Esophagus	11.8 nTPM
Lymph node	9.6 nTPM
Stomach	8.9 nTPM
Bone marrow	7.9 nTPM
Spleen	5.4 nTPM
Kidney	5.2 nTPM
Skin	1.7 nTPM

Ciliated cells	30.1 nTPM
Bronchus	56.7 nTPM
Lung	34.2 nTPM
Fallopian tube	21.4 nTPM
Endometrium	8.0 nTPM

Club cells	24.3 nTPM
Bronchus	41.0 nTPM
Prostate	17.6 nTPM
Lung	14.1 nTPM

Endothelial cells	4.5 nTPM
Pancreas	20.7 nTPM
Tongue	10.0 nTPM
Placenta	9.7 nTPM
Salivary gland	8.7 nTPM
Thymus	5.7 nTPM
Endometrium	4.9 nTPM
Prostate	3.6 nTPM
Breast	3.5 nTPM
Vascular	3.0 nTPM
Esophagus	2.6 nTPM
Lung	2.0 nTPM
Fallopian tube	1.5 nTPM
Skin	1.4 nTPM
Skeletal muscle	1.1 nTPM
Testis	0.9 nTPM
Heart muscle	0.9 nTPM
Ovary	0.7 nTPM
Liver	0.0 nTPM

Enteroendocrine cells	1.1 nTPM
Rectum	3.4 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Fibroblasts	1.4 nTPM
Lung	5.5 nTPM
Pancreas	3.9 nTPM
Placenta	1.8 nTPM
Salivary gland	1.7 nTPM
Skeletal muscle	1.4 nTPM
Stomach	1.4 nTPM
Prostate	1.3 nTPM
Vascular	1.1 nTPM
Breast	1.0 nTPM
Fallopian tube	0.9 nTPM
Heart muscle	0.7 nTPM
Thymus	0.7 nTPM
Adipose tissue	0.6 nTPM
Esophagus	0.4 nTPM
Skin	0.2 nTPM
Liver	0.0 nTPM

Granulocytes	2.9 nTPM
Lung	7.1 nTPM
Fallopian tube	1.7 nTPM
Tongue	0.0 nTPM

Intestinal goblet cells	0.1 nTPM
Rectum	0.4 nTPM
Colon	0.0 nTPM
Small intestine	0.0 nTPM

Lymphatic endothelial cells	5.1 nTPM
Fallopian tube	10.1 nTPM
Ovary	0.0 nTPM

Macrophages	2.5 nTPM
Thymus	8.6 nTPM
Tongue	6.1 nTPM
Vascular	5.3 nTPM
Spleen	4.0 nTPM
Salivary gland	3.2 nTPM
Adipose tissue	2.6 nTPM
Endometrium	2.5 nTPM
Skin	2.2 nTPM
Skeletal muscle	2.2 nTPM
Fallopian tube	2.1 nTPM
Kidney	1.8 nTPM
Prostate	1.7 nTPM
Breast	1.5 nTPM
Esophagus	1.3 nTPM
Lung	1.2 nTPM
Bone marrow	1.0 nTPM
Testis	0.0 nTPM
Pancreas	0.0 nTPM
Stomach	0.0 nTPM

Paneth cells	1.6 nTPM
Small intestine	3.5 nTPM
Rectum	1.5 nTPM
Colon	0.0 nTPM

Basal prostatic cells	4.2 nTPM
Prostate	4.2 nTPM

Basal respiratory cells	18.2 nTPM
Bronchus	18.2 nTPM

Basal squamous epithelial cells	3.3 nTPM
Esophagus	3.3 nTPM

Cholangiocytes	9.5 nTPM
Liver	9.5 nTPM

Plasma cells	5.8 nTPM
Fallopian tube	15.4 nTPM
Salivary gland	11.2 nTPM
Esophagus	10.4 nTPM
Thymus	3.2 nTPM
Liver	2.5 nTPM
Bone marrow	1.5 nTPM
Stomach	1.3 nTPM
Spleen	0.7 nTPM

Schwann cells	0.7 nTPM
Vascular	1.6 nTPM
Adipose tissue	0.4 nTPM
Esophagus	0.0 nTPM

Serous glandular cells	6.0 nTPM
Tongue	8.8 nTPM
Salivary gland	3.2 nTPM

Smooth muscle cells	0.9 nTPM
Tongue	3.0 nTPM
Liver	1.7 nTPM
Breast	1.6 nTPM
Endometrium	1.4 nTPM
Vascular	1.4 nTPM
Prostate	1.2 nTPM
Fallopian tube	1.0 nTPM
Salivary gland	0.9 nTPM
Thymus	0.9 nTPM
Placenta	0.8 nTPM
Skin	0.6 nTPM
Skeletal muscle	0.2 nTPM
Adipose tissue	0.0 nTPM
Esophagus	0.0 nTPM
Lung	0.0 nTPM
Ovary	0.0 nTPM

Suprabasal keratinocytes	28.6 nTPM
Tongue	55.5 nTPM
Skin	1.8 nTPM

T-cells	10.8 nTPM
Salivary gland	27.5 nTPM
Thymus	23.7 nTPM
Lung	19.7 nTPM
PBMC	16.8 nTPM
Tongue	15.8 nTPM
Adipose tissue	15.3 nTPM
Breast	12.8 nTPM
Skeletal muscle	11.3 nTPM
Vascular	10.5 nTPM
Skin	9.8 nTPM
Esophagus	9.7 nTPM
Fallopian tube	9.3 nTPM
Endometrium	8.0 nTPM
Prostate	7.4 nTPM
Lymph node	6.3 nTPM
Liver	5.0 nTPM
Spleen	5.0 nTPM
Bone marrow	4.2 nTPM
Colon	3.9 nTPM
Kidney	2.7 nTPM
Stomach	2.1 nTPM

Undifferentiated cells	0.8 nTPM
Rectum	1.0 nTPM
Small intestine	0.9 nTPM
Colon	0.6 nTPM

Amygdala excitatory	15.6 nTPM
Hypothalamus	23.1 nTPM
Thalamus	18.1 nTPM
Basal ganglia	17.7 nTPM
Cerebral cortex	13.6 nTPM
Amygdala	10.6 nTPM
Hippocampus	10.4 nTPM

Astrocyte	4.2 nTPM
Spinal cord	8.8 nTPM
Medulla oblongata	8.4 nTPM
Hypothalamus	6.3 nTPM
Cerebral cortex	4.7 nTPM
Pons	4.0 nTPM
Hippocampus	3.7 nTPM
Amygdala	2.7 nTPM
Cerebellum	2.5 nTPM
Thalamus	2.1 nTPM
Midbrain	1.8 nTPM
Basal ganglia	1.7 nTPM

Bergmann glia	1.1 nTPM
Medulla oblongata	2.1 nTPM
Cerebellum	1.0 nTPM
Pons	0.0 nTPM

Central nervous system macrophage	1.2 nTPM
Basal ganglia	1.5 nTPM
Cerebral cortex	1.5 nTPM
Hypothalamus	1.5 nTPM
Hippocampus	1.4 nTPM
Thalamus	1.4 nTPM
Medulla oblongata	1.2 nTPM
Amygdala	1.0 nTPM
Cerebellum	1.0 nTPM
Midbrain	1.0 nTPM
Spinal cord	0.9 nTPM
Pons	0.8 nTPM

Cerebellar inhibitory	33.2 nTPM
Cerebellum	43.4 nTPM
Spinal cord	35.7 nTPM
Midbrain	35.5 nTPM
Medulla oblongata	26.0 nTPM
Pons	25.6 nTPM

Cge interneuron	22.3 nTPM
Hypothalamus	30.7 nTPM
Cerebral cortex	23.4 nTPM
Basal ganglia	21.9 nTPM
Amygdala	21.4 nTPM
Hippocampus	21.1 nTPM
Thalamus	20.4 nTPM
Midbrain	17.1 nTPM

Choroid plexus epithelial cell	7.7 nTPM
Basal ganglia	12.2 nTPM
Hippocampus	8.3 nTPM
Medulla oblongata	7.5 nTPM
Thalamus	2.7 nTPM

Committed oligodendrocyte precursor	3.8 nTPM
Basal ganglia	8.8 nTPM
Medulla oblongata	6.5 nTPM
Thalamus	5.0 nTPM
Cerebral cortex	4.4 nTPM
Hippocampus	4.1 nTPM
Amygdala	3.4 nTPM
Midbrain	3.4 nTPM
Hypothalamus	2.7 nTPM
Pons	1.8 nTPM
Cerebellum	1.6 nTPM
Spinal cord	0.0 nTPM

Deep-layer corticothalamic and 6b	26.6 nTPM
Hypothalamus	36.7 nTPM
Midbrain	36.6 nTPM
Basal ganglia	24.5 nTPM
Amygdala	21.9 nTPM
Cerebral cortex	21.3 nTPM
Hippocampus	18.6 nTPM

Deep-layer intratelencephalic	16.8 nTPM
Hypothalamus	25.1 nTPM
Cerebral cortex	15.6 nTPM
Hippocampus	15.2 nTPM
Amygdala	14.6 nTPM
Basal ganglia	13.5 nTPM

Deep-layer near-projecting	22.7 nTPM
Hypothalamus	33.4 nTPM
Basal ganglia	22.5 nTPM
Amygdala	21.8 nTPM
Cerebral cortex	20.2 nTPM
Hippocampus	15.9 nTPM

Eccentric medium spiny neuron	12.5 nTPM
Hypothalamus	16.6 nTPM
Cerebral cortex	13.6 nTPM
Amygdala	13.0 nTPM
Thalamus	12.3 nTPM
Basal ganglia	12.0 nTPM
Hippocampus	7.5 nTPM

Endothelial cell	1.3 nTPM
Basal ganglia	2.8 nTPM
Cerebral cortex	2.6 nTPM
Medulla oblongata	2.1 nTPM
Thalamus	1.7 nTPM
Cerebellum	1.5 nTPM
Hypothalamus	1.2 nTPM
Amygdala	1.1 nTPM
Hippocampus	0.6 nTPM
Pons	0.6 nTPM
Midbrain	0.0 nTPM
Spinal cord	0.0 nTPM