Single cell type - GSKIP - 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.	GSKIP
Gene descriptionⁱ Full gene name according to HGNC.	GSK3B interacting 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.	6

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 - Unknown 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	Cell type enhanced (Early spermatids, Late spermatids, Distal enterocytes)
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: Cell type enhanced (Early spermatids, Late spermatids, Distal enterocytes)

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

GSKIP is part of cluster 34 Spermatids - Unknown function with confidenceⁱ 1
366 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
C2orf88	Chromosome 2 open reading frame 88	0.7704	34
MAPK3	Mitogen-activated protein kinase 3	0.7045	53
GOLM1	Golgi membrane protein 1	0.6616	34
MAPRE3	Microtubule associated protein RP/EB family member 3	0.6557	34
CARD18	Caspase recruitment domain family member 18	0.6492	34
PLAC8L1	PLAC8 like 1	0.6450	34
FAM104A	Family with sequence similarity 104 member A	0.6306	34
KIF2B	Kinesin family member 2B	0.6295	34
FABP12	Fatty acid binding protein 12	0.6267	34
TIMD4	T cell immunoglobulin and mucin domain containing 4	0.6265	34
DUX4	Double homeobox 4	0.6263	34
FAM71D	Family with sequence similarity 71 member D	0.6230	34
ZNF345	Zinc finger protein 345	0.6149	34
AKIRIN1	Akirin 1	0.6144	34
NT5C1B-RDH14	NT5C1B-RDH14 readthrough	0.6137	34

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	12.6 nTPM
Breast	13.3 nTPM
Adipose tissue	11.9 nTPM

Alveolar cells type 1	12.8 nTPM
Lung	12.8 nTPM

Alveolar cells type 2	7.4 nTPM
Lung	7.4 nTPM

Astrocytes	5.9 nTPM
Brain	5.9 nTPM

B-cells	24.8 nTPM
Spleen	32.2 nTPM
Colon	27.1 nTPM
PBMC	27.1 nTPM
Stomach	25.5 nTPM
Breast	24.1 nTPM
Lymph node	23.9 nTPM
Kidney	23.8 nTPM
Bone marrow	23.7 nTPM
Liver	21.1 nTPM
Adipose tissue	19.5 nTPM

Dendritic cells	17.9 nTPM
Breast	21.5 nTPM
Adipose tissue	16.4 nTPM
PBMC	16.0 nTPM

Endothelial cells	17.4 nTPM
Pancreas	34.7 nTPM
Skin	21.1 nTPM
Eye	21.0 nTPM
Esophagus	19.7 nTPM
Testis	19.0 nTPM
Ovary	19.0 nTPM
Breast	16.9 nTPM
Placenta	16.5 nTPM
Lung	15.6 nTPM
Endometrium	15.0 nTPM
Skeletal muscle	14.3 nTPM
Heart muscle	11.6 nTPM
Prostate	10.4 nTPM
Liver	8.2 nTPM

Fibroblasts	12.1 nTPM
Placenta	20.9 nTPM
Skin	19.6 nTPM
Stomach	14.9 nTPM
Breast	11.8 nTPM
Esophagus	11.3 nTPM
Prostate	10.3 nTPM
Lung	10.1 nTPM
Skeletal muscle	9.8 nTPM
Ovary	9.5 nTPM
Adipose tissue	7.9 nTPM
Heart muscle	7.0 nTPM

Intestinal goblet cells	73.0 nTPM
Colon	83.6 nTPM
Small intestine	78.3 nTPM
Rectum	57.0 nTPM

Macrophages	16.8 nTPM
PBMC	27.3 nTPM
Pancreas	23.0 nTPM
Stomach	20.5 nTPM
Testis	20.3 nTPM
Kidney	19.6 nTPM
Esophagus	18.9 nTPM
Bone marrow	18.8 nTPM
Breast	17.9 nTPM
Prostate	17.2 nTPM
Ovary	13.8 nTPM
Skeletal muscle	12.8 nTPM
Endometrium	11.6 nTPM
Lung	11.4 nTPM
Spleen	10.4 nTPM
Adipose tissue	8.2 nTPM

Paneth cells	102.9 nTPM
Colon	128.4 nTPM
Small intestine	105.1 nTPM
Rectum	75.2 nTPM

Plasma cells	22.6 nTPM
Esophagus	36.9 nTPM
Stomach	23.8 nTPM
Bone marrow	23.0 nTPM
Spleen	19.8 nTPM
Adipose tissue	9.7 nTPM

Respiratory ciliated cells	28.6 nTPM
Bronchus	41.2 nTPM
Lung	16.0 nTPM

Smooth muscle cells	16.5 nTPM
Bronchus	37.6 nTPM
Pancreas	34.8 nTPM
Skin	21.2 nTPM
Ovary	15.8 nTPM
Esophagus	15.5 nTPM
Prostate	13.1 nTPM
Endometrium	10.6 nTPM
Breast	10.6 nTPM
Adipose tissue	7.7 nTPM
Skeletal muscle	7.3 nTPM
Heart muscle	7.1 nTPM

T-cells	24.4 nTPM
Kidney	43.1 nTPM
Skin	38.7 nTPM
Stomach	33.8 nTPM
Colon	30.4 nTPM
Bone marrow	29.4 nTPM
Breast	28.6 nTPM
Prostate	28.4 nTPM
Spleen	28.0 nTPM
Esophagus	26.2 nTPM
Adipose tissue	24.5 nTPM
Liver	22.9 nTPM
Lymph node	20.6 nTPM
PBMC	18.7 nTPM
Endometrium	17.3 nTPM
Skeletal muscle	12.2 nTPM
Ovary	6.7 nTPM
Lung	6.1 nTPM

Basal keratinocytes	45.2 nTPM
Skin	45.2 nTPM

Basal prostatic cells	24.2 nTPM
Prostate	24.2 nTPM

Basal respiratory cells	27.6 nTPM
Bronchus	27.6 nTPM

Basal squamous epithelial cells	19.9 nTPM
Esophagus	19.9 nTPM

Undifferentiated cells	69.1 nTPM
Colon	102.8 nTPM
Small intestine	59.4 nTPM
Rectum	45.0 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