Expression of PHGDH in cancer - Summary

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.	PHGDH
Gene descriptionⁱ Full gene name according to HGNC.	Phosphoglycerate dehydrogenase
Protein classⁱ Assigned HPA protein class(es) for the encoded protein(s). Read more	Disease related genes Enzymes 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	Intracellular
Number of transcriptsⁱ Number of protein-coding transcripts from the gene as defined by Ensembl.	10

HUMAN PROTEIN ATLAS INFORMATIONⁱ

RNA categoryⁱ

Consensus (human tissue):	Low tissue specificity Detected in all
HPA (cell line):	Cell line enhanced (SK-MEL-30) Detected in many
TCGA (cancer tissue):	Low cancer specificity Detected in all

Protein evidenceⁱ

Evidence at protein level

Protein expression
normal tissueⁱ

General cytoplasmic expression with nuclear expression in several tissues.

IMMUNOHISTOCHEMISTRY DATA RELIABILITY
Data reliability descriptionⁱ Standardized explanatory sentences with additional information required for full understanding of the protein expression profile, based on knowledge-based and secretome-based annotation.	Medium consistency between antibody staining and RNA expression data. Pending external verification.
Reliability score - normal tissuesⁱ A reliability score is manually set for all genes and indicates the level of reliability of the analyzed protein expression pattern based on available RNA-seq data, protein/gene characterization data and immunohistochemical data from one or several antibodies with non-overlapping epitopes. The reliability score is based on the 44 normal tissues analyzed, and if there is available data from more than one antibody, the staining patterns of all antibodies are taken into consideration during evaluation. The reliability score is divided into Enhanced, Supported, Approved, or Uncertain, and is displayed on both Tissue Atlas and Pathology Atlas. Read more	Enhanced
Antibodiesⁱ Antibodies used for this assay. Click on an antibody for more information.	HPA021241 , HPA024031 , CAB003681 , CAB068216
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PROGNOSTIC SUMMARYⁱ

Prognostic marker in endometrial cancer (unfavorable) and glioma (favorable)

Endometrial cancer p<0.001 Glioma p<0.001

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RNA EXPRESSION OVERVIEWⁱ RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).
TCGA datasetⁱ RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. Normal distribution across the dataset is visualized with box plots, shown as median and 25th and 75th percentiles. Points are displayed as outliers if they are above or below 1.5 times the interquartile range. To access cancer specific RNA and prognostic data, click on the cancer name. The cancer types are color-coded according to which type of normal organ the cancer originates from. Read more RNA cancer category: Low cancer specificity

PROTEIN EXPRESSIONⁱ Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset. For histological reference, visit the histological dictionary.
Colorectal cancer Breast cancer Prostate cancer Lung cancer Skin cancer
PROTEIN EXPRESSION SUMMARYⁱ For each cancer, color-coded bars indicate the percentage of patients (maximum 12 patients) with high and medium protein expression level. The cancer types are color-coded according to which type of normal organ the cancer originates from. Low or not detected protein expression results in a white bar. Mouse-over function shows details about expression level and normal tissue of origin. The images and annotations can be accessed by clicking on the cancer name or protein expression bar. If more than one antibody is analyzed, the tabs at the top of the staining summary section can be used to toggle between the different antibodies. Read more
Organ Expression Alphabetical
HPA021241 HPA024031 CAB003681 CAB068216 Moderate to strong cytoplasmic and occasional nuclear staining in most cancer tissues. Moderate to strong cytoplasmic or nuclear staining in most cancer tissues often with a negative fraction of cells. Most lymphomas and several melanomas were negative. Gliomas and most cases of melanoma, colorectal, breast, male and female genital cancers as well as several urothelial cancers showed moderate to strong cytoplasmic positivity. Other cancers were weakly stained or negative. Most cancer tissues displayed strong cytoplasmic immunoreactivity with additional nuclear staining in several cases. Several lymphomas along with few melanomas and pancreatic cancers were negative.