We use cookies to enhance the usability of our website. If you continue, we'll assume that you are happy to receive all cookies. More information. Don't show this again.
WDR54
HPA
RESOURCES
  • TISSUE
  • BRAIN
  • SINGLE CELL
  • SUBCELLULAR
  • CANCER
  • BLOOD
  • CELL LINE
  • STRUCTURE & INTERACTION
ABOUT
  • INTRODUCTION
  • HISTORY
  • ORGANIZATION
  • PUBLICATIONS
  • ANTIBODY SUBMISSION
  • ANTIBODY AVAILABILITY
  • ACKNOWLEDGMENTS
  • CONTACT
NEWS
  • NEWS ARTICLES
  • PRESS ROOM
LEARN
  • DICTIONARY
  • PROTEIN CLASSES
  • PROTEIN EVIDENCE
  • METHODS
  • EDUCATIONAL VIDEOS
DATA
  • DOWNLOADABLE DATA
  • PUBLICATION DATA
  • RELEASE HISTORY
HELP
  • ANTIBODY VALIDATION
  • ASSAYS & ANNOTATION
  • DISCLAIMER
  • HELP & FAQ
  • PRIVACY STATEMENT
  • LICENCE & CITATION
Fields »
Search result

Field
Term
Gene name
Class
Subclass
Class
Keyword
Chromosome
External id
Tissue
Cell type
Expression
Antibody panel
Tissue
Main location
Patient ID
Annotation
Tissue
Category
Tau score
Cluster
Reliability
Brain region
Category
Tau score
Brain region
Category
Tau score
Brain region
Category
Tau score
Cluster
Reliability
Tissue
Cell type
Enrichment
Cell type
Category
Tau score
Cell type
Category
Tau score
Cell type
Category
Tau score
Cell lineage
Category
Tau score
Cluster
Cluster
Location
Searches
Location
Cell line
Class
Type
Phase
Reliability
Cancer
Prognosis
Cancer
Category
Cancer
Category
Tau score
Cluster
Variants
Interacting gene (ensg_id)
Type
Number of interactions
Pathway
Category
Score
Score
Score
Validation
Validation
Validation
Validation
Antibodies
Data type
Column


  • SUMMARY

  • TISSUE

  • BRAIN

  • SINGLE CELL

  • SUBCELL

  • CANCER

  • BLOOD

  • CELL LINE

  • STRUCT & INT

  • WDR54
SINGLE CELL SINGLE CELL TYPES TISSUE CELL TYPE SINGLE NUCLEI BRAIN IMMUNE CELLS EXPRESSION CLUSTER TISSUES Show tissue menu
ADIPOSE TISSUE ADRENAL GLAND BONE MARROW BRAIN BREAST BRONCHUS COLON ENDOMETRIUM ESOPHAGUS EYE
FALLOPIAN TUBE HEART MUSCLE KIDNEY LIVER LUNG LYMPH NODE OVARY PANCREAS PBMC PITUITARY GLAND
PLACENTA PROSTATE RECTUM SALIVARY GLAND SKELETAL MUSCLE SKIN SMALL INTESTINE SPLEEN STOMACH TESTIS
THYMUS THYROID GLAND TONGUE VASCULAR
Single cell type
Tabula sapiens
Tissue cell type
Cell type proteome
Cell type enrichment
Brain cells
Immune cells
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.

WDR54
Gene descriptioni

Full gene name according to HGNC.

WD repeat domain 54
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.

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.

Ciliated cells - Cilium assembly (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 (Ciliated cells, Spermatocytes, Late spermatids, Cone photoreceptor cells, Rod photoreceptor 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.

0.54
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.

Cell type enhanced (Ependymal cell)
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

Overview of the different datasets included in the Single Cell resource.

Single cell type
Cell type enrichment
Single nuclei - Brain
Immune cells
Expression clustering
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 (Ciliated cells, Spermatocytes, Late spermatids, Cone photoreceptor cells, Rod photoreceptor 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

A summary of normalized single nuclei RNA (nTPM) from the brain single nuclei. Color-coding is based on cell type groups (as defined in the single cell type data representing the whole body), in this case separated into the main cell categories of neuron, glial cells, endothelial cells, fibroblasts and muscle cell (vascular smooth muscle cells and pericytes).

The data is based on Siletti K et al. (2023) public data.

Single nuclei cluster types
RNA brain cluster specificity: Cell type enhanced (Ependymal cell)
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

The RNA data was used to cluster genes according to their expression across samples. The resulting clusters have been manually annotated to describe common features in terms of function and specificity. The annotation of the cluster is displayed together with a confidence score of the gene's assignment to the cluster. The confidence is calculated as the fraction of times the gene was assigned to this cluster in repeated calculations and is reported between 0 to 1, where 1 is the highest possible confidence. The clustering results are shown in a UMAP, where the cluster this gene was assigned to is highlighted as a colored area in which most of the cluster genes reside. A table shows the 15 most similar genes in terms of expression profile.

SINGLE CELL TYPE
WDR54 is part of cluster 42 Ciliated cells - Cilium assembly with confidencei

Confidence is the fraction of times a gene was assigned to the cluster in repeated clustering, and therefore reflects how strongly associated it is to the cluster. A confidence of 1 indicates that the gene was assigned to this cluster in all repeated clusterings.

1
429 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.

RSPH1 Radial spoke head component 1 0.8653 42
CFAP52 Cilia and flagella associated protein 52 0.8499 42
PIFO Primary cilia formation 0.8380 42
C22orf15 Chromosome 22 open reading frame 15 0.8365 42
LRRC23 Leucine rich repeat containing 23 0.8331 42
RSPH9 Radial spoke head component 9 0.8273 42
PRR29 Proline rich 29 0.8247 42
DNAH12 Dynein axonemal heavy chain 12 0.8211 42
SPEF1 Sperm flagellar 1 0.8178 42
AK7 Adenylate kinase 7 0.8168 42
C20orf85 Chromosome 20 open reading frame 85 0.8134 42
C7orf57 Chromosome 7 open reading frame 57 0.8078 42
DYDC2 DPY30 domain containing 2 0.7958 42
TMEM190 Transmembrane protein 190 0.7888 42
FAM216B Family with sequence similarity 216 member B 0.7881 42
IMMUNE CELLS
WDR54 is part of cluster 13 Non-specific - Mitochondria with confidencei

Confidence is the fraction of times a gene was assigned to the cluster in repeated clustering, and therefore reflects how strongly associated it is to the cluster. A confidence of 1 indicates that the gene was assigned to this cluster in all repeated clusterings.

0.89
458 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.

ZNF789 Zinc finger protein 789 1.0000 13
KANK1 KN motif and ankyrin repeat domains 1 1.0000 13
TMEM201 Transmembrane protein 201 1.0000 13
PRKRA Protein activator of interferon induced protein kinase EIF2AK2 1.0000 13
NHP2 NHP2 ribonucleoprotein 1.0000 13
ERGIC3 ERGIC and golgi 3 0.9762 13
PLEKHG4 Pleckstrin homology and RhoGEF domain containing G4 0.9762 13
COA4 Cytochrome c oxidase assembly factor 4 homolog 0.9762 13
CHID1 Chitinase domain containing 1 0.9762 13
TBCA Tubulin folding cofactor A 0.9762 13
ESD Esterase D 0.9762 13
NME1-NME2 NME1-NME2 readthrough 0.9762 13
PMEPA1 Prostate transmembrane protein, androgen induced 1 0.9762 13
PRXL2A Peroxiredoxin like 2A 0.9762 13
STMN1 Stathmin 1 0.9762 13
 

Contact

  • NEWS ARTICLES
  • PRESS ROOM

The Project

  • INTRODUCTION
  • ORGANIZATION
  • PUBLICATIONS

The Human Protein Atlas

  • DOWNLOADABLE DATA
  • LICENCE & CITATION
  • HELP & FAQ
The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.


contact@proteinatlas.org