Dictionary

The purpose of the dictionary is to facilitate the interpretation and use of the image-based data available in the Human Protein Atlas, but also to serve as a tool for training and understanding histology, pathology and cell biology. The dictionary contains three main parts; normal tissue histology, pathology, and cell structure. The parts of the dictionary covering normal tissues and pathology are based on full tissue sections stained with hematoxylin-eosin (HE) and representative high-resolution images can be explored at different magnifications. The dictionary covering cell structure is built around antibody-based stainings of proteins in cell lines using immunofluorescence and confocal microscopy. Representative examples have been selected to illustrate stainings of different organelles and subcellular compartments that are annotated in the Cell Atlas.

NORMAL TISSUE HISTOLOGYi

The normal histology section of the dictionary is based on representative sections from human tissues. Tissues were collected and treated in conformance with Swedish laws and regulations and obtained from the Clinical Department of Pathology, Uppsala University Hospital, Sweden. In accordance, all human tissue samples have been anonymized. Examples of normal tissue histology have been selected from regions in these surgical specimens where morphology appears as normal.

The aim of this section is to educate readers about histology of normal tissues, which provide important and basic information for our understanding of biology and medicine.

PATHOLOGYi

The cancer section of the dictionary is based on representative hematoxylin-eosin (HE) stained sections from clinical tumor tissues. Tissues were collected and treated in conformance with Swedish laws and regulations and obtained from the Clinical Department of Pathology, Uppsala University Hospital, Sweden. In accordance, all human tissue samples have been anonymized. The dictionary includes 20 different tumor types whereof many are various subtypes that differ in both morphology and clinical behavior.

Cancer is a broad group of approximately 200 diseases and is signified by dysregulated and autonomous cell growth with attainable spread and growth in distant organs. The aim of this section is to educate readers about the histology of cancer tissues. Hallmarks of cancer are described here, and cancer statistics from relevant international and Swedish databases are summarized here.

CELL STRUCTUREi

The cell structure section of the dictionary provides brief descriptions of the cellular compartments annotated in the Cell Atlas, including their staining characteristics upon immunofluorescence in human cell lines and representative examples. The cells are stained with an in-house generated HPA-antibody (green) and counterstained with markers for microtubules (red), the endoplasmic reticulum (yellow) and the nucleus (blue). Confocal microscopy has been used to provide high-resolution, four-color images. The aim of the cell structure section is to provide an overview of the subcellular compartments and how to recognize them in cells stained by immunofluorescence.

Complementary annotation dictionaries using antibodies found in the Human Protein Atlas are available as PDF-documents:
Immunohistochemistry annotation dictionary: screen usage (15MB), printing (95MB).