Tissue expression of SHMT2 - Summary - The Human Protein Atlas

Protein class

Protein class the gene product belongs to according to selected gene lists. List of protein classes.

Predicted localization

Protein localization predicted from several bioinformatic algorithms. More info...

Number of transcripts

Number of protein-coding transcribed from this gene as defined by Ensembl.

RNA tissue category

The RNA tissue category is based on mRNA expression levels in 32 different tissues (RNA assay description). The categories include: tissue enriched, group enriched, tissue enhanced, expressed in all, not detected, and mixed. RNA tissue category is calculated separately both for internally generated Human Protein Atlas (HPA) RNA-seq data, as well as RNA-seq data from the Genotype-Tissue Expression (GTEx) consortium.

Protein evidence

Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence or iv) not available.

Protein localization

A summary of the overall protein expression pattern across the analyzed tissues. The summary is based on knowledge-based annotation (Annotation description). For genes pending knowledge-based annotation, the protein localization refers to the antibody staining pattern.

"RNA-based expert annotation gave inconconclusive results" is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry-data to yield a reliable estimation of the protein expression profile.

Data reliability description

Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile. Currently, not all genes have been analyzed by knowledge-based annotation, indicated by "Pending RNA-based expert annotation", when applicable.

Data reliability

Data reliability score (score description), divided into supportive (premium) or uncertain (not premium), is based on consistency between the staining pattern of one antibody or several antibodies with RNA-seq data and available gene/protein characterization data.

Below to the right is an overview of RNA and protein expression data generated in the HPA project. Analyzed tissues are divided into 13 color-coded groups according to common functional features. For each group, a list of included tissues is accessed by clicking on group name, group symbol, RNA bar or protein bar. Subsequent selection of a particular tissue in this list links to the image data page.

Images of selected tissues give a visual summary of the protein expression profile below to the left. The gray human body in the middle provides links to a histology dictionary when clicking on any part of the figure.

RNA expression (FPKM)

RNA–seq results generated in HPA are reported as number of Fragments Per Kilobase gene model and Million reads (FPKM). The assay is described more in detail in Assays & Annotation.

Protein expression (score)

Each bar represents the highest expression score found in a particular group of tissues. For proteins where the antibody staining pattern has been analyzed by knowledge-based annotation, protein expression scores are based on a best estimate of the "true" protein expression, described more in detail under Assays & annotation. For genes that are pending this extended review, the protein expression scores correspond to the staining profile of the used antibody. For genes where more than one antibody has been used, a common score is set displaying the estimated "true" protein expression.

Protein expression data is shown for each of the 44 tissues. Color-coding is based on 13 tissue groups, each consisting of tissues with common functional features. Mouse-over function shows protein score for analyzed cell types found in a selected tissue. To access image data click on tissue name or bar. Annotation of protein expression is described in detail in Assays & annotation.

For genes with available protein data for which a knowledge-based annotation could not be performed, no protein expression data is displayed in the protein expression data overview, however, all immunohistochemical images are still available and the annotation data can be found under Primary data.

HPA dataset

RNA-seq data from 32 tissues are reported as mean FPKM (Fragments Per Kilobase gene model and Million reads), corresponding to mean values of the different individual samples from each tissue type. Color-coding is based on 13 tissue groups, each consisting of tissues with common functional features. To access sample data, click on tissue name or bar. The RNA-seq assay is described in detail in Assays & Annotation.

RNA tissue category HPA

HPA RNA tissue category (category description) is calculated based on mRNA expression levels in 32 different tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, not detected and mixed.

GTEx dataset

RNA-seq data from 28 tissues are reported as median RPKM (reads per kilobase per million mapped reads), generated by the Genotype-Tissue Expression (GTEx) consortium. More information can be found in Assays & Annotation.

RNA tissue category GTEx

GTEx RNA tissue category (category description) is calculated based on mRNA expression levels in 28 different tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, not detected and mixed.

Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.

The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.

At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.

Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50) (read more).

If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.

Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.

The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.

The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.

The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.

The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0 and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.

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