Single cell type - LIN7C - 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.	LIN7C
Gene descriptionⁱ Full gene name according to HGNC.	Lin-7 homolog C, crumbs cell polarity complex component
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.	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. Read more	Epithelial cell types - Mixed function (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	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. Read more	Low immune cell specificity
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	Detected in all
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 all
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: Low cell type specificity

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

LIN7C is part of cluster 22 Epithelial cell types - Mixed function with confidenceⁱ 1
298 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
USP38	Ubiquitin specific peptidase 38	0.4867	44
RMND5A	Required for meiotic nuclear division 5 homolog A	0.4620	6
KLF5	Kruppel like factor 5	0.4508	22
LYSMD3	LysM domain containing 3	0.4467	24
FUBP3	Far upstream element binding protein 3	0.4342	5
NIPAL1	NIPA like domain containing 1	0.4340	22
PRRG4	Proline rich and Gla domain 4	0.4317	22
FOXN1	Forkhead box N1	0.4264	61
RAB40B	RAB40B, member RAS oncogene family	0.4211	44
HOXD13	Homeobox D13	0.4207	53
AQP3	Aquaporin 3 (Gill blood group)	0.4190	22
COG3	Component of oligomeric golgi complex 3	0.4176	27
TAF13	TATA-box binding protein associated factor 13	0.4147	41
SLC30A1	Solute carrier family 30 member 1	0.4146	44
EIF1AX	Eukaryotic translation initiation factor 1A X-linked	0.4139	39

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	23.8 nTPM
Adipose tissue	27.3 nTPM
Breast	20.4 nTPM

Alveolar cells type 1	28.9 nTPM
Lung	28.9 nTPM

Alveolar cells type 2	13.1 nTPM
Lung	13.1 nTPM

Astrocytes	10.7 nTPM
Brain	10.7 nTPM

B-cells	14.7 nTPM
Spleen	22.5 nTPM
Stomach	22.3 nTPM
Adipose tissue	20.6 nTPM
Bone marrow	19.6 nTPM
Lymph node	15.6 nTPM
Liver	14.7 nTPM
Colon	12.8 nTPM
Breast	12.1 nTPM
PBMC	7.1 nTPM
Kidney	0.0 nTPM

Dendritic cells	21.8 nTPM
PBMC	27.9 nTPM
Adipose tissue	27.5 nTPM
Breast	9.9 nTPM

Endothelial cells	22.9 nTPM
Heart muscle	46.6 nTPM
Prostate	41.2 nTPM
Endometrium	27.0 nTPM
Skin	24.3 nTPM
Skeletal muscle	22.8 nTPM
Ovary	21.0 nTPM
Eye	19.4 nTPM
Pancreas	19.3 nTPM
Testis	18.4 nTPM
Liver	18.3 nTPM
Breast	18.2 nTPM
Esophagus	17.5 nTPM
Placenta	14.2 nTPM
Lung	12.5 nTPM

Fibroblasts	21.0 nTPM
Adipose tissue	29.0 nTPM
Prostate	26.8 nTPM
Stomach	23.7 nTPM
Lung	22.4 nTPM
Skeletal muscle	22.3 nTPM
Skin	21.3 nTPM
Heart muscle	20.9 nTPM
Ovary	20.8 nTPM
Esophagus	16.3 nTPM
Breast	14.3 nTPM
Placenta	13.7 nTPM

Intestinal goblet cells	38.6 nTPM
Rectum	49.2 nTPM
Colon	35.8 nTPM
Small intestine	30.8 nTPM

Macrophages	17.2 nTPM
Adipose tissue	25.9 nTPM
Spleen	22.8 nTPM
Endometrium	21.2 nTPM
Kidney	20.4 nTPM
Pancreas	20.4 nTPM
Esophagus	18.9 nTPM
Lung	18.8 nTPM
Ovary	18.7 nTPM
Skeletal muscle	18.3 nTPM
Bone marrow	17.5 nTPM
Prostate	15.0 nTPM
Stomach	14.7 nTPM
Testis	14.0 nTPM
Breast	11.8 nTPM
PBMC	0.0 nTPM

Paneth cells	25.1 nTPM
Rectum	39.2 nTPM
Small intestine	26.3 nTPM
Colon	9.9 nTPM

Plasma cells	21.4 nTPM
Esophagus	30.7 nTPM
Stomach	24.1 nTPM
Bone marrow	21.4 nTPM
Adipose tissue	15.5 nTPM
Spleen	15.2 nTPM

Respiratory ciliated cells	15.7 nTPM
Bronchus	19.6 nTPM
Lung	11.7 nTPM

Smooth muscle cells	25.7 nTPM
Heart muscle	32.8 nTPM
Esophagus	29.4 nTPM
Skin	29.3 nTPM
Prostate	29.1 nTPM
Adipose tissue	28.3 nTPM
Bronchus	25.4 nTPM
Skeletal muscle	23.9 nTPM
Ovary	23.9 nTPM
Breast	21.6 nTPM
Endometrium	20.4 nTPM
Pancreas	18.3 nTPM

T-cells	16.6 nTPM
Adipose tissue	27.3 nTPM
Esophagus	26.2 nTPM
Stomach	24.5 nTPM
Colon	20.9 nTPM
Spleen	20.1 nTPM
Skin	18.8 nTPM
Bone marrow	18.6 nTPM
Lymph node	17.4 nTPM
Endometrium	16.6 nTPM
Skeletal muscle	16.2 nTPM
Kidney	15.1 nTPM
Prostate	14.2 nTPM
Breast	13.6 nTPM
Liver	12.7 nTPM
PBMC	12.0 nTPM
Lung	4.5 nTPM
Ovary	4.5 nTPM

Basal prostatic cells	31.5 nTPM
Prostate	31.5 nTPM

Basal squamous epithelial cells	21.1 nTPM
Esophagus	21.1 nTPM

Cholangiocytes	25.8 nTPM
Liver	25.8 nTPM

Collecting duct cells	27.6 nTPM
Kidney	27.6 nTPM

Undifferentiated cells	33.9 nTPM
Rectum	38.6 nTPM
Colon	36.5 nTPM
Small intestine	26.4 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