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and dragging, click on an object for more info, right-click (ctrl-click for Mac) for menu.
The following bookmark (i.e., a URL or Web link) allows you to redisplay the current diagram with its active highlighted objects (not Omics Data highlighting) at the current zoom level.
Generated Bookmark:You can click and drag the bookmark:
- on the bookmark toolbar of your browser
- into your favorite bookmarks menu
- on your desktop
- into a new open window of your browser
- anywhere else accepted by your operating system.
Enter names and unique identifiers (aka frame ids) of genes, proteins, metabolites, and/or reactions to highlight them in the cellular overview. Then click the highlight button. To avoid ambiguities, enter the names on separate lines, or use the semi-colon character (';') to delimit names (e.g. thymine ; adenine).
You can also enter expression data (i.e., a numerical value) after each name and/or frame id. In that case, the Cellular Omics Viewer will be started to display the result.
Enter object names and/or frame ids below with or without expression data.
| Object | Icon Shape |
|---|---|
| Amino Acids | Pointing up triangle |
| Carbohydrates | Square |
| Proteins | Diamond |
| Purines | Vertical ellipse |
| Pyrimidines | Horizontal ellipse |
| Cofactors | Pointing down triangle |
| tRNAS | Tee |
| Other | Circle |
| Phosphorylated | Filled |
The Omics Viewer can be used for:
- Microarray Expression Data: Reaction lines (and protein icons, where present) are color-coded according to the relative or absolute expression level of the gene that codes for the enzyme that catalyzes that reaction step. The Omics Viewer allows a scientist to interpret the results of gene-expression experiments in a pathway context.
- Proteomics Data: Reaction lines (and protein icons, where present) are color-coded according to the concentration of the enzyme that catalyzes that reaction step.
- Metabolomics Data: Compound icons are color-coded according to the concentration of the compound.
- Reaction Flux Data: Reaction lines are color-coded according to reaction flux values.
- Other Experimental Data: Any experiment, high-throughput or otherwise, in which data values are assigned to genes, proteins, reactions or metabolites can be viewed in a pathway context using the Omics Viewer.
Click here to go to the Webinar page, where you can watch the Comparative and Omics Tools in BioCyc instructional videos.
More information about the Omics Viewer, including sample datafiles and displays.
The Omics Viewer takes as input a tab-delimited data file that is stored on your local computer. The file contains relative or absolute data for a set of genes, proteins, reactions, metabolites, or some combination. Each row of the file contains data for a single gene, protein, reaction, or metabolite, and begins with the object name, ID or EC number. You may choose to display either data from a single column, the ratio of two columns, or a time series animation of multiple columns. Data columns other than those specified are ignored.
For an example data file, see here
In addition to the color-coded Cellular Overview diagram, the resulting display includes a histogram and basic statistics computed from the supplied data.