Tissue expression of CDH1 - Staining in skin

The protein expression bar, with the units none (n), low (l), medium (m) and high (h), is based on a best estimate of the "true" protein expression for proteins where the antibody staining pattern has been analyzed by knowledge-based annotation. For genes where more than one antibody has been used, a common score is set. For details, see Assays & annotation.

RNA expression shows average values based on RNA-seq data generated by HPA or the Genotype-Tissue Expression (GTEx) consortium.

HPA RNA expression data are reported as number of Fragments Per Kilobase gene model and Million reads (FPKM). For details, see Assays & annotation.

GTEx RNA expression data are reported as reads per kilobase per million mapped reads (RPKM). For details, see Assays & annotation.

The detailed normal tissue page shows images of the stained tissue, together with antibody staining/expression level of the cell types. If a knowledge-based annotated protein expression is provided, this is reported for each cell type at the top of the page and the staining level of the individual antibodies is given underneath each antibody ID.

Samples from up to three different individuals have been stained for each antibody. The gender, age and tissue characterization are reported for each individual (patient) and are viewable when clicking on the image for magnification.

The images can be clicked for an enlarged view that can be panned. From the enlarged view, all stained images for all antibodies can be browsed (represented by miniature images). The miniature image with an orange overlay is the currently displayed image.

For histological reference, view skin in the histological dictionary.

The RNA-seq details section shows detailed information about the individual samples used for the transcript profiling and results of the RNA-seq analysis.

On top the transcript layout for all coding and non-coding transcripts of the gene, with introns scaled down by a factor 20, is shown. Untranslated regions (UTRs) of protein-coding transcripts are colored gray.

Information about each individual sample is listed below, including gender, age, a tissue section image and estimated fractions of cell types. FPKM (Fragments Per Kilobase of exon per Million fragments mapped) values give a quantification of the gene abundance which is comparable between different genes and samples. The FPKM is calculated as the sum of FPKMs of all protein-coding transcripts.

The plots show the mapped read coverage along all exons and introns of the gene, thereby revealing which exons are expressed and at what relative levels. The levels are normalized by total library size and scaled to fit the highest peak of all samples to the height of the plot. Thus these plots should not be used to compare abundances between different samples or genes, but rather as an indication of which transcripts are expressed and as a quality control.

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

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. RPKM values of the individual samples are presented next to the box plot.

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