Cell line - VPS9D1 - The Human Protein Atlas

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VPS9D1

SUMMARY

TISSUE

BRAIN

SINGLE CELL

TISSUE CELL

PATHOLOGY

IMMUNE

BLOOD

SUBCELL

CELL LINE

METABOLIC

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.	VPS9D1
Gene descriptionⁱ Full gene name according to HGNC.	VPS9 domain containing 1
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.	3

HUMAN PROTEIN ATLAS INFORMATIONⁱ Summary of RNA expression and protein localization based on data generated within the Human Protein Atlas project.
Cell line expression clusterⁱ The RNA data was used to cluster genes according to their expression across cell lines. 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	T47d - Mammary gland (mainly)
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

CELL LINESⁱ

Organ

Expression

Alphabetical

EXPRESSION CLUSTERING & CORRELATIONⁱ

VPS9D1 is part of cluster 6 T47d - Mammary gland with confidenceⁱ 1
293 genes in cluster

Go to interactive expression cluster page

15 nearest neighbours based on cell line 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
ENDOV	Endonuclease V	0.6676	6
PNMA1	PNMA family member 1	0.6538	40
GAA	Glucosidase alpha, acid	0.6152	6
RARA	Retinoic acid receptor alpha	0.6113	40
CCDC170	Coiled-coil domain containing 170	0.6107	40
RHBDF1	Rhomboid 5 homolog 1	0.6055	40
HCN2	Hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2	0.6012	40
GRPR	Gastrin releasing peptide receptor	0.5978	6
C5AR2	Complement component 5a receptor 2	0.5972	6
ESR1	Estrogen receptor 1	0.5897	6
NCAM2	Neural cell adhesion molecule 2	0.5789	6
LTBP3	Latent transforming growth factor beta binding protein 3	0.5771	11
ABCA2	ATP binding cassette subfamily A member 2	0.5767	6
TCTN2	Tectonic family member 2	0.5713	6
SPATA2L	Spermatogenesis associated 2 like	0.5678	40

Contact

contact@proteinatlas.org

The Project

The Human Protein Atlas

The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.