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CELLPEDIA Reference Manual
Contents
CELLPEDIA is a repository database for current knowledge about human cells. It contains various types of information, such as cell morphologies, gene expression, and literature references. The major role of CELLPEDIA is to provide a digital dictionary of human cells for the biomedical field. The homepage of CELLPEDIA displays the data statistics, a few examples of cell images and a minimum spanning tree of gene expression profiles of cells or tissues.
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CELLPEDIA defines its own enhanced cell taxonomy for physically distinct cells, establishing a hierarchical structure of up to eight levels from organs (or tissues) to cells. It presents a combination of both conventional cell taxonomy and their physical locations.
In total, about 2,300 types of differentiated human cells are listed and assigned unique cell taxonomy keys.
Similarly, stem cells and progenitor cells are classified into about 70 taxonomy keys.
Some of the differentiated cells and stem cells are interconnected based on the cell differentiation information by taxonomy keys.
*Not all cell types contain data yet.
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We have collected cell images corresponding to our human cell taxonomy keys to provide visual information about the cells.
The cell images are primarily collected by submission from various laboratories and manually checked by the curators for their quality and tissue origins.
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Reference journal articles for each cell taxonomy key are manually curated by the authors to glean existing knowledge about mammalian cells.
The contents of the journal articles are represented by a concise sentence incorporating the most important information.
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We collected gene expression data from such public databases as the Gene Expression Omnibus and ArrayExpress.
We also provide a data submission page for gene expression data.
Due to limitations in the current techniques for single-cell analysis and available data, we have so far accumulated gene expression data obtained from tissues or multiple cells.
To avoid confusion, we have added a "Population" category in the gene expression data table to provide information of the data resource.
"Heterogeneous" means that the gene expression data are measured from a heterogeneous cell population.
"Multiple" means that the data are measured from unique but multiple cells.
"Single" means that the data are measured from a single cell.
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The integrated page added three more information on cells; morphological parameters, the OBO Cell Type Ontology and cell neighborhood links besides the above three primary data and cell taxonomy, and displays them together to provide an environment of information links among all parts of accumulated cell knowledge.
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With each cell image, morphological parameters and their values are added for computational purposes,
making it easier to analyze cell morphological differences.
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The OBO organization provides the ontology for approximately 1,500 types of cells from various organisms, including vertebrates.
We incorporate human-related cell ontological terms into our integrated pages to provide formal names of cell types under the defined vocabulary.
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CELLPEDIA provides binary(parent-child) relationships involved in cell differentiation.
collected from textbooks and journals, as the "cell neighborhood".
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The following figure shows an example of deducing cell differentiation or transdifferentiation pathways from the integrated page of hepatocyte using cell neighborhood links.
It is noteworthy that distant relationships between cells can be deduced by following consecutive neighborhood links.
For example, the differentiation route of liver progenitor cells to pancreatic beta cells is determined by successively following the links from "liver progenitor cell to hepatocyte" and from "hepatocyte to pancreatic beta cell".
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Keyword search is available for cell taxonomy, three primary data and OBO cell type ontology.
Simply putting your words in the blank and clicking the submit button will give you a list of data that contain the words in a few seconds.
The system can accept the keywords containing following special characters as delimiters (@#$%^&*()|=+>:[],.).
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W. Fujibuchi, L. Kiseleva, T. Taniguchi, and P. Horton, Development of Cell Knowledge Base and Prediction of Cell Types and Characteristics
by Gene Expression Profiles, 2005-BIO-2;33-37 SIG Meeting, Information Processing Society of Japan, 2005.
A. Hatano, H. A. Moesa, H. Chiba, T. Taniguchi, S. Nagaie, K. Yamanegi, and W. Fujibuchi, CELLPEDIA: Comprehensive human cell database toward cell differentiation analysis, 2010-BIO-20; 1-4 SIG Meeting, Information Processing Society of Japan, 2010.
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© National Institute of Advanced Industrial Science and Technology