Single cell type - TOM1L1 - The Human Protein Atlas

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.	TOM1L1
Gene descriptionⁱ Full gene name according to HGNC.	Target of myb1 like 1 membrane trafficking protein
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. Read more	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	14

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. Read more	Spermatids - Spermatogenesis (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. Read more	Cell type enhanced (Late spermatids, Distal tubular cells)
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. Read more	Not detected in immune cells
Immune cell distributionⁱ The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Read more	Not detected
Cell line specificityⁱ RNA specificity category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into six different categories (enriched, group enriched, enhanced, low specificity and not detected) according to their RNA expression levels across the panel of cell lines. Read more	Low cell line specificity
Cell line distributionⁱ RNA distribution category based on RNA sequencing data from all cell lines in the Human Protein Atlas. Genes are classified into five different categories (detected in all, detected in many, detected in some, detected in single and not detected) according to their pattern of detected RNA expression across the panel of cell lines. Read more	Detected in many
Protein evidenceⁱ Evidence score for genes based on UniProt protein existence (UniProt evidence); a Human Protein Atlas antibody- or RNA based score (HPA evidence); and evidence based on PeptideAtlas (MS evidence). The avaliable scores are evidence at protein level, evidence at transcript level, no evidence, or not avaliable. Read more	Evidence at protein level

SINGLE CELL TYPESⁱ A summary of 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 Group Expression Alphabetical RNA single cell type specificity: Cell type enhanced (Late spermatids, Distal tubular cells)

SINGLE CELL TISSUES OVERVIEWⁱ An overview of all tissues where single cell type expression has been analyzed. Each tissue name and corresponding UMAP plot is clickable and redirects to the selected tissue.
Adipose tissue Bone marrow Brain Breast Bronchus Colon Endometrium Esophagus Eye Heart muscle Kidney Liver Lung Lymph node Ovary Pancreas Placenta Prostate Rectum Skeletal muscle Skin Small intestine Spleen Stomach Testis

EXPRESSION CLUSTERING & CORRELATIONⁱ

TOM1L1 is part of cluster 25 Spermatids - Spermatogenesis with confidenceⁱ 1
458 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on single cell type 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. Read more	Clusterⁱ ID of the expression cluster of the neighboring gene. Read more
SLC25A10	Solute carrier family 25 member 10	0.5543	67
NEURL1	Neuralized E3 ubiquitin protein ligase 1	0.5186	25
WASF1	WASP family member 1	0.5099	25
ACSM1	Acyl-CoA synthetase medium chain family member 1	0.5035	25
MAPK13	Mitogen-activated protein kinase 13	0.4934	30
FER1L6	Fer-1 like family member 6	0.4911	16
C17orf100	Chromosome 17 open reading frame 100	0.4866	25
CHST8	Carbohydrate sulfotransferase 8	0.4800	25
EPHA10	EPH receptor A10	0.4742	25
PEX10	Peroxisomal biogenesis factor 10	0.4721	25
LRRC28	Leucine rich repeat containing 28	0.4677	25
IGSF22	Immunoglobulin superfamily member 22	0.4577	39
PTPMT1	Protein tyrosine phosphatase mitochondrial 1	0.4517	25
SEC16B	SEC16 homolog B, endoplasmic reticulum export factor	0.4456	25
CHDH	Choline dehydrogenase	0.4453	67

SINGLE CELL TISSUESⁱ Single cell RNA levels of annotated cell type clusters are shown separately for each analyzed tissue. For easier navigation across tissues, use the above Single cell tissue overview, where each tissue name and UMAP plot is clickable and redirects to the selected tissue, alternatively the grey browser on the left side of the window. Barchart shows nTPM levels in each annotated cluster of single cells. To the left, a UMAP plot illustrates the RNA expression profile. The tissue name and plots are clickable and redirect to a more detailed interactive page. Color-coding is based on cell type groups, each consisting of cell types with functional features in common. Please note that the same cell type may be found in several clusters.
Cluster Expression Alphabetical Adipose tissue
Cluster Expression Alphabetical Bone marrow
Cluster Expression Alphabetical Brain
Cluster Expression Alphabetical Breast
Cluster Expression Alphabetical Bronchus
Cluster Expression Alphabetical Colon
Cluster Expression Alphabetical Endometrium
Cluster Expression Alphabetical Esophagus
Cluster Expression Alphabetical Eye
Cluster Expression Alphabetical Heart muscle
Cluster Expression Alphabetical Kidney
Cluster Expression Alphabetical Liver
Cluster Expression Alphabetical Lung
Cluster Expression Alphabetical Lymph node
Cluster Expression Alphabetical Ovary
Cluster Expression Alphabetical Pancreas
Cluster Expression Alphabetical Placenta
Cluster Expression Alphabetical Prostate
Cluster Expression Alphabetical Rectum
Cluster Expression Alphabetical Skeletal muscle
Cluster Expression Alphabetical Skin
Cluster Expression Alphabetical Small intestine
Cluster Expression Alphabetical Spleen
Cluster Expression Alphabetical Stomach
Cluster Expression Alphabetical Testis

BLOODⁱ

Single cell data

Cluster

Expression

Alphabetical

PBMC

Flow sorted data

Lineage

Expression

Alphabetical

CELL LINESⁱ

Organ

Expression

Alphabetical

Adipocytes	1.1 nTPM
Breast	1.2 nTPM
Adipose tissue	1.0 nTPM

Alveolar cells type 1	22.4 nTPM
Lung	22.4 nTPM

Alveolar cells type 2	21.6 nTPM
Lung	21.6 nTPM

Astrocytes	15.3 nTPM
Brain	15.3 nTPM

B-cells	1.9 nTPM
Kidney	14.3 nTPM
Colon	1.6 nTPM
Liver	1.3 nTPM
Breast	1.3 nTPM
Stomach	0.5 nTPM
PBMC	0.0 nTPM
Adipose tissue	0.0 nTPM
Lymph node	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Dendritic cells	0.8 nTPM
Breast	2.2 nTPM
Adipose tissue	0.2 nTPM
PBMC	0.0 nTPM

Endothelial cells	0.9 nTPM
Breast	3.8 nTPM
Heart muscle	1.9 nTPM
Skeletal muscle	1.6 nTPM
Prostate	1.5 nTPM
Testis	1.4 nTPM
Endometrium	1.1 nTPM
Skin	0.7 nTPM
Esophagus	0.5 nTPM
Ovary	0.2 nTPM
Eye	0.0 nTPM
Liver	0.0 nTPM
Lung	0.0 nTPM
Placenta	0.0 nTPM
Pancreas	0.0 nTPM

Fibroblasts	4.2 nTPM
Lung	11.1 nTPM
Placenta	7.3 nTPM
Prostate	7.0 nTPM
Ovary	7.0 nTPM
Esophagus	3.0 nTPM
Stomach	3.0 nTPM
Skin	2.0 nTPM
Heart muscle	1.8 nTPM
Skeletal muscle	1.8 nTPM
Breast	1.4 nTPM
Adipose tissue	0.5 nTPM

Intestinal goblet cells	55.2 nTPM
Small intestine	67.0 nTPM
Rectum	60.1 nTPM
Colon	38.6 nTPM

Macrophages	3.1 nTPM
PBMC	27.3 nTPM
Kidney	6.1 nTPM
Stomach	2.9 nTPM
Lung	2.6 nTPM
Endometrium	2.0 nTPM
Ovary	1.9 nTPM
Breast	1.8 nTPM
Testis	1.2 nTPM
Skeletal muscle	0.8 nTPM
Adipose tissue	0.4 nTPM
Prostate	0.0 nTPM
Pancreas	0.0 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Paneth cells	30.4 nTPM
Rectum	40.4 nTPM
Small intestine	37.6 nTPM
Colon	13.2 nTPM

Plasma cells	0.7 nTPM
Adipose tissue	2.7 nTPM
Stomach	0.9 nTPM
Esophagus	0.0 nTPM
Bone marrow	0.0 nTPM
Spleen	0.0 nTPM

Respiratory ciliated cells	20.1 nTPM
Lung	26.2 nTPM
Bronchus	14.1 nTPM

Smooth muscle cells	6.5 nTPM
Ovary	13.4 nTPM
Prostate	11.0 nTPM
Breast	8.3 nTPM
Endometrium	6.2 nTPM
Esophagus	6.2 nTPM
Pancreas	5.9 nTPM
Bronchus	5.6 nTPM
Skin	5.2 nTPM
Adipose tissue	4.1 nTPM
Skeletal muscle	2.7 nTPM
Heart muscle	2.5 nTPM

T-cells	1.2 nTPM
Kidney	6.2 nTPM
Endometrium	5.7 nTPM
Liver	2.7 nTPM
Breast	2.2 nTPM
Colon	1.9 nTPM
Skin	0.9 nTPM
Skeletal muscle	0.8 nTPM
PBMC	0.3 nTPM
Stomach	0.3 nTPM
Adipose tissue	0.2 nTPM
Bone marrow	0.1 nTPM
Lung	0.0 nTPM
Prostate	0.0 nTPM
Ovary	0.0 nTPM
Esophagus	0.0 nTPM
Lymph node	0.0 nTPM
Spleen	0.0 nTPM

Basal keratinocytes	15.8 nTPM
Skin	15.8 nTPM

Basal prostatic cells	17.2 nTPM
Prostate	17.2 nTPM

Basal respiratory cells	21.3 nTPM
Bronchus	21.3 nTPM

Basal squamous epithelial cells	19.4 nTPM
Esophagus	19.4 nTPM

Undifferentiated cells	42.8 nTPM
Small intestine	61.2 nTPM
Rectum	40.5 nTPM
Colon	26.5 nTPM

Adipose tissue

Bone marrow

Brain

Breast

Bronchus

Colon

Endometrium

Esophagus

Eye

Heart muscle

Kidney

Liver

Lung

Lymph node

Ovary

Pancreas

Placenta

Prostate

Rectum

Skeletal muscle

Skin

Small intestine

Spleen

Stomach

Testis

PBMC