Additional file 1: Table S1. of Comparison, alignment, and synchronization of cell line information between CLO and EFO

EFO cell lines drawn from external sources. In the initial step of the EFO-CLO comparison and alignment process, there are 428 and 20 EFO cell lines which were imported from Cell Line Ontology and 20 in BRENDA Tissue and Enzyme Source Ontology respectively. These 448 EFO cell lines were excluded from the entire mapping process. File is stored in Microsoft Excel spreadsheet (xlsx) format. (XLSX 47 kb

Additional file 2: Table S2. of Comparison, alignment, and synchronization of cell line information between CLO and EFO

Final EFO-CLO alignment result. The 874 EFO-CLO mapped cell lines aligned and merged into CLO (Tab. 1 in the excel file) and 344 EFO unique immortalized permanent cell lines added to CLO (Tab. 2 in the excel file). File is stored in Microsoft Excel spreadsheet (xlsx) format. (XLSX 54 kb

Additional file 1: of Using OWL reasoning to support the generation of novel gene sets for enrichment analysis

A complete over-representation analysis for RCV gene sets against GTEx tissue type transcriptomes. The analysis is displayed as a heat map with RCV on the Y-axis, GTEx on the X-axis, over-respresentation in blue and under-respresentation in red. Both axes are clustered for similarity (see Methods for details). (PDF 91 kb

Additional file 1: of Reporting phenotypes in mouse models when considering body size as a potential confounder

Supplementary Methods. (DOCX 21 kb

Principal components.

<p>On top, the first two principal components. The panel on the left illustrates the clear separation along the X-axis of the hematopoietic and non-hematopoietic material containing samples from both tissues and cell lines. The non-solid region includes blood, bone marrow, lymph nodes, tonsil, osteoclasts, spleen, sputum, thymus gland, bronchoalveolar lavage cells and derived cell lines. An elongated cluster including incompletely differentiated cells is also found. In the right panel, the Y-axis separates cell lines (top), neoplasias (middle) and non-neoplastic diseases (bottom), whereas normal tissues overlap with all three. The panel in the bottom shows the data for the first (X-axis) and third components (Y-axis). The hematopoietic axis (X-axis) allows detaching leukaemias from other blood neoplasias. Cell lines derived from brain tumours can be distinguished from their tissues of origin along this axis as well. The Y-axis detaches non-neoplastic central nervous system samples from tumoral ones, and separates myelomas from lymphomas.</p

Genes mapping to the top 100 probesets.

<p>Genes mapping to the top 100 probesets.</p

Expression level changes across tissue types and disease status.

<p>Distribution of the number of groups for which there is a clear change in the expression level of the probeset. The values are quantified by having either the group mean minus the group standard deviation above the overall mean or the group mean plus the group standard deviation below the overall mean.</p

Group sizes in paired tissues.

<p>Group sizes in paired tissues.</p

Additional file 2: of Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

The list of journals mined for disease-phenotype assocations. (PDF 13 kb

Additional file 1: of Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

URLs to the supplementary downloadable result files for text mining results (IBD, Autoimmunity, Skeletal disorders, and Metabolism disorders). (PDF 18 kb