Sarcoma Project Web Site Overview
The site is intended to allow interaction with sets of data regarding a set of human cell lines, mostly sarcoma-derived but including some "normal" cell lines. The categories of available data are concentration/response data for a set of approved and investigational cancer drugs, Affymetrix Exon Array data (aggregated by UniGene cluster), and NanoString microRNA expression data.
Lists of the recognized search terms for each data category are available.
Data can be searched by any combination of NSC compound identifier and drug names for concentration/response data, GeneCard (HUGO) gene symbol for Affymetrix Exon Array data, or miRbase microRNA identifier for NanoString data.
Searches can be restricted to a subset of the cell lines or sarcoma panels, which identify subgroups of the cell lines by sarcoma type. There is also a "normal" panel for the expression data. By default, data for all cell lines and panels will be returned. If any cell line and/or panel are selected then only data for those cell lines and panels will be returned. This selection is INCLUSIVE: Data for all cell lines which are in the selected panels will be returned along with data for any selected cell lines which are not in the selected panels.
A search result is a single value for a cell line and a data type.
For a combination of a cell line and a compound this value is the median IC50, and fitted curve parameters, which aggregates all replicate concentration/response experiments for a given cell line and compound.
For a combination of a cell line and an Affymetrix Exon Identifier this value is a normalized expression value.
For a combination of a cell line and a NanoString Identifier this value is a normalized count.
Alternative Data Formats
Data can be accessed in several different formats:
where each row is a single datum for a cell line and one of the data categories.
which is color-coded crosstabulation of the data with a single row for each cell line and column groupings by compounds, Affymetrix Identifiers or NanoString Identifiers, with colors determined by the data values
Unit Delta Heat Map
which is color-coded crosstabulation of the data with a single row for each cell line and column groupings by compounds, Affymetrix Identifiers or NanoString Identifier, with the data in each column scaled from -1 to 1 and with colors determined by that scaling.
which are horizontal bar charts representing crosstabulations of the difference between each data value and the mean of all data values for a given compound, Affymetrix Identifier or NanoString Identifier.
Links to trigger actions on the data
Depending on the data format, various actions can be triggered.
In each row in the Data Table layout for compound data there is a link to the to the concentration/response data for individual experiments underlying the single reported aggregate determination of IC50.
In each row in the Data Table layout for Affymetrix and NanoString data there are links to web resources for the identifiers.
In each column of the HeatMap, UnitDelta Heat Map, and set of Mean Graphs there are links to use the underlying data as a reference pattern for running COMPARE analyses against all of the sarcoma project data.
Additionally, for compound data there are also links to to render the median concentration/response data for all cell lines in an "AllPlot" graph or as a set of plots grouped by cell panel in a "PanelPlot."
The underlying data for each format can be downloaded as Excel or CSV files.
The heat maps, mean graphs, concentration/response curves, AllPlots, and PanelPlots can all be downloaded as .png images.
Images on web pages
On the web pages the concentration/response curves and mean graphs are rendered as Html "canvas" elements which are not accessible to Screen Readers. In addition to the option to download the data, listed above, data tables, and charts (heatMaps, meanGraphs, concentration/response curves) are preceded by an "Alternate Table" link which renders a table intended to be accessible to users of screen readers.
Web Page Layout
There are sets of navigation buttons on the web pages grouped by sections. Navigation buttons are active or disabled depending which data categories were populated during the most-recent search, and in which format the data are being presented.
Project Site Navigation
section is on every page. It includes navigation buttons to: the Home/Search Page, Compound Data, Affymetrix Data, NanoString Data, and the Project Documentation and Downloads page.
section will follow. There are navigation buttons to: Data Table, Heat Map, Unit Delta Heat Map, and Mean Graphs.
section will follow. This summarizes the layout of the rest of the page, depending on the selected data format that. The format of the data is described as well as any actions on the data which can be triggered.
Export Data or Images
section will follow. Data can be downloaded in Excel or CSV (comma-separated values) format, images in .png format.
The rest of the page will contain content specific to the data type and data format. Headers for data tables and charts will include a link to a ScreenReader accessible version of the underlying data.