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 Prior to staining with hematoxylin-eosin (HE), the tissue samples were formalin fixed, paraffin embedded and cut in 4 µm thin sections, which were then fixed on glass slides. Scanned images of these sections can be explored interactively, at different magnifications. Annotations of various structures and corresponding descriptions guide the visitor across the tissue sections.
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.		Brain Cerebral cortex Hippocampus Caudate Cerebellum Endocrine tissues Thyroid gland Parathyroid gland Adrenal gland Respiratory system Nasopharynx Bronchus Lung Proximal digestive tract Oral mucosa Salivary gland Esophagus Gastointestinal tract Stomach Duodenum Small intestine Colon Rectum Liver & Gallbladder Liver Gallbladder Pancreas Pancreas Kidney & Urinary bladder Kidney Urinary bladder Male tissues Testis Epididymis Seminal vesicle Prostate Female tissues Vagina Ovary Fallopian tube Endometrium Cervix, Uterine Placenta Breast Muscle tissues Heart muscle Smooth muscle Skeletal muscle Connective & soft tissue Adipose tissue Skin Skin Bone marrow & Lymphoid tissues Bone marrow Lymph node Tonsil Spleen Appendix

PATHOLOGYⁱ Prior to staining with hematoxylin-eosin (HE), the tissue samples were formalin fixed, paraffin embedded and cut in 4 µm thin sections, which were then fixed on glass slides. Scanned images of these sections can be explored interactively, at different magnifications. Annotations of various structures and corresponding descriptions guide the visitor across the tissue sections.
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.		Brain tumors Glioma Head & neck tumors Head and neck cancer Endocrine tumors Thyroid cancer Neuroendocrine tumors Lung tumors Lung cancer Abdominal tumors Stomach cancer Colorectal cancer Liver cancer Pancreatic cancer Uro-genital tumors Renal cancer Urothelial cancer Testis cancer Prostate cancer Ovarian cancer Endometrial cancer Cervical cancer Breast tumors Breast cancer Skin tumors Melanoma Basal cell and squamous cell cancer Lymphoid tumors Lymphoma

CELL STRUCTUREⁱ Immunofluorescent images of formaldehyde-fixed cell lines are shown. Three different organelle markers are displayed as different channels in the multicolor images - nucleus stained in blue, microtubules in red and ER in yellow. The various cell structures that are demonstrated are always shown in the green channel using an antibody found in the Human Protein Atlas. The antibody id is linked to the corresponding Cell Atlas protein page. By using the "toggle channels"-buttons, the different channels can be turned on and off. Most cell structures can be highlighted in the cell illustration by hovering over them with the exception of the aggresome. Cytoplasmic bodies are highlighted as substructures of cytosol; cytokinetic bridge, midbody, midbody ring and mitotic spindle are highlighted as microtubules, cell junctions are highlighted as plasma membrane and nucleus is highlighted as nucleoplasm.
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.		Cytoplasm Actin filaments Aggresome Centriolar satellite Centrosome Cleavage furrow Cytokinetic bridge Cytoplasmic bodies Cytosol Focal adhesion sites Intermediate filaments Microtubule ends Microtubules Midbody Midbody ring Mitochondria Mitotic spindle Rods & rings Nucleus Kinetochore Mitotic chromosome Nuclear bodies Nuclear membrane Nuclear speckles Nucleoli Nucleoli fibrillar center Nucleoli rim Nucleoplasm Secretory Cell junctions Endoplasmic reticulum Endosomes Golgi apparatus Lipid droplets Lysosomes Peroxisomes Plasma membrane Vesicles

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