Catalpa bignonioides Walt.

原著和名: アメリカキササゲ科名: ノウゼンカズラ科 = Bignoniaceae採集地: 千葉県 千葉市 千葉大学 (下総 千葉市 千葉大学)採集日: 1979/6/15採集者: 萩庭丈壽整理番号: JH026901国立科学博物館整理番号: TNS-VS-97690

Additional file 2: of A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer

and 2–1 show detailed process of MP score computation. (DOCX 106 kb

Additional file 4: of A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer

shows detailed description of identified drug candidates for breast and prostate cancer. (XLSX 140 kb

Grewia rhombifolia Kanehira et Sasaki

原著和名: ウヲトリギ エノキウツギ科名: シナノキ科 = Tiliaceae採集地: 千葉県 千葉市 (下総 千葉市)採集日: 1964/7/1採集者: 萩庭丈壽整理番号: JH026860国立科学博物館整理番号: TNS-VS-97686

Additional file 11: Figure S6. of A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer

Titration curves of cell viability under treatment of Fluphenazine. Viability of MCF10A, MCF7 and SUM 149 cells exposed to Fluphenazine with concentrations ranging from 3.125 μM to 100 μM after 24 h incubation. The relative viability was calculated as relative viability = (experimental absorbance - background absorbance)/ (absorbance of untreated controls - background absorbance of untreated controls) × 100 % (means ± SD, n = 3). (PPTX 55 kb

List of repositioning candidates for three cancers.

<p>FDA approved compounds are marked with (*); Compounds showing duality with (^§); Color of candidates match to the FDA-approved drug for the corresponding cancer, e.g. Tamoxifen is FDA-approved drug for breast cancer and is predicted as a repositioning candidate for acute myeloid leukemia. Words such as “Ph2” in the bracket of some predictions indicate that the corresponding drug is in the phase 2 clinical trial according to ClinicalTrial.gov at the time when the manuscript is prepared.</p

The comparison of up- or down-regulated genes between each pair of the gene-expression signature from the CMAP and the gene-expression signature from the GEO.

<p>The parameter k indicates the preselected number of up- or down-regulated genes. UC (Top ranking genes in a Cancer type) and UB (Top ranking genes with a Bioactive compound) represent up-regulated genes in the GEO and the CMAP respectively, whereas DC (Botom ranking genes in a Cancer type) and DB (Bottom ranking gene with a Bioactive compound) represent down-regulated genes in the GEO and the CMAPs respectively.</p

Bioactive compounds identified with optimal parameters.

<p>Among total 1309 compounds in CMAP, 913 (510 are FDA approved drugs) were used in this study. Supporting evidence is based on direct literature search or the ClinicalTrial.gov database. “Total compounds in CMAP” indicates the number of compounds used in the CMAP. “Compounds that are FDA drugs” counts number of FDA approved drugs in the “Total compounds in CMAP”. “Predicted FDA drugs for target disease” counts in-use drugs for the target disease in CMAP.</p

Over-represented pathways for breast cancer and myelogenous leukemia.

<p>The horizontal axis lists the pathways and the vertical axis represents the percentage of identified compounds that perturb the pathway. <b>AD</b>: Adherens junction, <b>B</b>: Bacterial invasion of epithelial cells, <b>E</b>: ErbB signaling pathway, <b>F</b>: Focal adhesion, <b>M</b>: Riboflavin metabolism, <b>N</b>: Nucleotide excision repair, <b>R</b>: Ribosome, <b>T</b>: Thiamine metabolism, <b>D</b>: Drug metabolism - cytochrome P450, <b>G</b>: Glycerolipid metabolism, <b>GL</b>: Glycerophospholipid metabolism, <b>GPI</b>: Glycosylphosphatidylinositol (GPI)-anchor biosynthesis, <b>VA</b>: Vascular smooth muscle contraction, <b>TGF</b>: TGF-βsignaling pathway, <b>C</b>: Cell cycle, <b>A</b>: Apoptosis, <b>TC</b>: T cell receptor signaling.</p

Metabolic exchange in a microbial ecosystem.

<p>Visualization of metabolic exchange between many organisms in a system is achieved through VisANT's multi-organism layout. The six organisms shown here are microbes selected because of their roles and abundance in the human gut. Metabolic flux was determined through a COMETS simulation involving all six microbes in a minimal D-glucose media. Each model is represented by a metanode, and in the center of the models are nutrients in the media that interact with the models. Nodes are color coded by their syntrophic influence, gray being nutrients involved in a potential syntrophy, red being nutrients which the microbes may be competing over, blue being nutrients which are produced by more than one organism, but consumed by none, and dark gray being nutrients which only have one model interacting with them. The network is simplified by hiding metabolite nodes that are not transported in/out by any model at this time point (normally displayed in white color), as well as metabolites not useful for biological interpretation of interactions, including biomass subcomponents (Protein_biosynthesis_e0, RNA_transcription_e0, and DNA_replication_e0) and highly connected ubiquitous metabolites (H2O_e0, H+_e0, Orthophosphate_e0). Minor manual rearrangement was conducted for the expanded network to improve clarity. Five of the six model metanodes are collapsed for clarity, but <i>H</i>. <i>pylori</i> is shown expanded, displaying the environmental exchange reactions. Nutrients of interest, Oxygen, D-Glucose, D-Galactose, (S)-Lactate, and Formate, have been labeled. Part of the L-Proline intracellular pathway has been expanded to exemplify VisANT’s capabilities.</p