The Human Protein Atlas—a tool for pathology

TLDR

Tissue‑based diagnostics are rapidly evolving, and immunohistochemistry provides additional diagnostic and prognostic information beyond morphology by revealing protein expression patterns in cancer. The authors created a comprehensive immunohistochemistry atlas (version 4) comprising over 5 million images of 5 011 proteins from 6 122 antibodies, with detailed antigen sequences, validation data, and a gene‑centric database that supports complex queries of expression, protein class, and chromosomal location. The Human Protein Atlas thus serves as a freely available resource for pathology‑based biomedical research, protein science, and biomarker discovery.

Abstract

Tissue-based diagnostics and research is incessantly evolving with the development of new molecular tools. It has long been realized that immunohistochemistry can add an important new level of information on top of morphology and that protein expression patterns in a cancer may yield crucial diagnostic and prognostic information. We have generated an immunohistochemistry-based map of protein expression profiles in normal tissues, cancer and cell lines. For each antibody, altogether 708 spots of tissues and cells are analysed and the resulting images and data are presented as freely available in the Human Protein Atlas (www.proteinatlas.org). The new version 4 of the atlas, including more than 5 million images of immunohistochemically stained tissues and cells, is based on 6122 antibodies, representing 5011 human proteins encoded by approximately 25% of the human genome. The gene-centric database includes a putative classification of proteins in various protein classes, both functional classes, such as kinases or transcription factors and project-related classes, such as candidate genes for cancer or cardiovascular diseases. For each of the internally generated antibodies, the exact antigen sequence is presented, together with a visualization of application-specific validation data, including a protein array assay, western blot analysis, immunohistochemistry and, in most cases, immunofluorescent-based confocal microscopy. The updated version also includes new search algorithms to allow complex queries regarding expression profiles, protein classes and chromosome location. Thus, the presented Human Protein Atlas provides a resource for pathology-based biomedical research, including protein science and biomarker discovery.