Single cell type - CFD - 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.	CFD
Gene descriptionⁱ Full gene name according to HGNC.	Complement factor D
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes Human disease related genes Plasma proteins Potential drug targets
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	Secreted
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	Fibroblasts - ECM organization (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	Group enriched (Fibroblasts, Leydig 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	Immune cell enhanced (basophil)
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	Group enriched (ASC diff, THP-1)
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
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. Read more	Protein predicted to be secreted

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: Group enriched (Fibroblasts, Leydig 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

CFD is part of cluster 50 Fibroblasts - ECM organization with confidenceⁱ 1
441 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
OMD	Osteomodulin	0.9522	50
CLEC3B	C-type lectin domain family 3 member B	0.9411	50
CCDC80	Coiled-coil domain containing 80	0.9410	50
XG	Xg glycoprotein (Xg blood group)	0.9378	50
GSN	Gelsolin	0.9376	50
CCN5	Cellular communication network factor 5	0.9343	50
PPDPFL	Pancreatic progenitor cell differentiation and proliferation factor like	0.9322	50
WNT11	Wnt family member 11	0.9256	50
COL6A6	Collagen type VI alpha 6 chain	0.9224	50
TMDD1	Transmembrane and death domain 1	0.9204	50
C5orf58	Chromosome 5 open reading frame 58	0.9095	50
H3Y1	H3.Y histone 1	0.9094	50
GDF10	Growth differentiation factor 10	0.9085	50
VEGFD	Vascular endothelial growth factor D	0.9078	50
CXCL12	C-X-C motif chemokine ligand 12	0.9063	50

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	857.8 nTPM
Adipose tissue	1156.4 nTPM
Breast	559.1 nTPM

Alveolar cells type 1	9.6 nTPM
Lung	9.6 nTPM

Alveolar cells type 2	23.3 nTPM
Lung	23.3 nTPM

Astrocytes	0.0 nTPM
Brain	0.0 nTPM

B-cells	19.2 nTPM
Breast	124.5 nTPM
PBMC	15.7 nTPM
Colon	14.4 nTPM
Kidney	14.3 nTPM
Liver	7.5 nTPM
Stomach	7.3 nTPM
Adipose tissue	5.5 nTPM
Lymph node	1.6 nTPM
Bone marrow	0.8 nTPM
Spleen	0.3 nTPM

Dendritic cells	40.0 nTPM
Breast	101.3 nTPM
Adipose tissue	14.9 nTPM
PBMC	4.0 nTPM

Endothelial cells	114.8 nTPM
Skin	705.8 nTPM
Skeletal muscle	400.8 nTPM
Lung	171.5 nTPM
Breast	105.2 nTPM
Heart muscle	82.4 nTPM
Endometrium	35.7 nTPM
Placenta	27.8 nTPM
Prostate	24.4 nTPM
Eye	19.4 nTPM
Testis	15.4 nTPM
Esophagus	13.6 nTPM
Liver	5.5 nTPM
Ovary	0.1 nTPM
Pancreas	0.0 nTPM

Fibroblasts	9365.5 nTPM
Adipose tissue	37905.1 nTPM
Breast	16524.2 nTPM
Skeletal muscle	13143.5 nTPM
Skin	10131.6 nTPM
Esophagus	8577.8 nTPM
Stomach	8322.8 nTPM
Prostate	5125.2 nTPM
Heart muscle	1850.8 nTPM
Placenta	1163.5 nTPM
Lung	222.3 nTPM
Ovary	53.5 nTPM

Intestinal goblet cells	8.7 nTPM
Colon	10.7 nTPM
Rectum	8.3 nTPM
Small intestine	7.1 nTPM

Macrophages	442.5 nTPM
Ovary	1826.8 nTPM
Skeletal muscle	1005.9 nTPM
Kidney	841.0 nTPM
Adipose tissue	436.4 nTPM
Esophagus	424.9 nTPM
Breast	369.9 nTPM
Stomach	348.7 nTPM
Bone marrow	294.9 nTPM
Spleen	265.4 nTPM
Testis	232.9 nTPM
Prostate	205.2 nTPM
Lung	187.8 nTPM
Endometrium	126.1 nTPM
Pancreas	58.7 nTPM
PBMC	13.6 nTPM

Paneth cells	64.8 nTPM
Colon	128.4 nTPM
Rectum	35.8 nTPM
Small intestine	30.0 nTPM

Plasma cells	41.0 nTPM
Adipose tissue	156.1 nTPM
Stomach	46.5 nTPM
Bone marrow	1.7 nTPM
Spleen	1.0 nTPM
Esophagus	0.0 nTPM

Respiratory ciliated cells	28.4 nTPM
Bronchus	33.6 nTPM
Lung	23.3 nTPM

Smooth muscle cells	530.2 nTPM
Adipose tissue	3904.3 nTPM
Skin	609.9 nTPM
Skeletal muscle	470.1 nTPM
Breast	320.7 nTPM
Prostate	311.4 nTPM
Heart muscle	66.7 nTPM
Esophagus	51.2 nTPM
Endometrium	46.5 nTPM
Pancreas	30.4 nTPM
Bronchus	19.4 nTPM
Ovary	1.1 nTPM

T-cells	82.8 nTPM
Skin	788.0 nTPM
Skeletal muscle	382.6 nTPM
Breast	53.4 nTPM
Endometrium	39.0 nTPM
Lung	33.4 nTPM
PBMC	20.1 nTPM
Esophagus	19.7 nTPM
Prostate	19.0 nTPM
Colon	10.0 nTPM
Ovary	8.9 nTPM
Stomach	7.6 nTPM
Adipose tissue	7.4 nTPM
Liver	6.2 nTPM
Bone marrow	6.0 nTPM
Kidney	2.7 nTPM
Lymph node	1.7 nTPM
Spleen	1.6 nTPM

Basal keratinocytes	785.5 nTPM
Skin	785.5 nTPM

Basal prostatic cells	49.0 nTPM
Prostate	49.0 nTPM

Basal respiratory cells	10.1 nTPM
Bronchus	10.1 nTPM

Basal squamous epithelial cells	17.1 nTPM
Esophagus	17.1 nTPM

Undifferentiated cells	21.0 nTPM
Colon	23.7 nTPM
Rectum	21.7 nTPM
Small intestine	17.5 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