Generate Bookmark for Cellular Overview
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.
Highlight Names or Frame Ids, With or Without Expression Data
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.
Cellular Overview Legend and Key Shapes
| 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 |
Highlighting by Pathway Name or Frame Id
Highlighting by Pathway Name Substring
Highlighting Pathway by Curation
Omics DataTable for selected Pathway Categories
Highlighting Pathways by Evidence
Highlighting by Compound Name or Frame Id
Highlighting by Compound Name Substring
Highlighting by Enzyme Name or Frame Id
Highlighting by Enzyme Name Substring
Highlighting by Gene Name or Frame Id
Highlighting by Gene Name Substring
Highlighting Genes by Regulon
Highlighting reactions by activators
Highlighting reactions by inhibitors
Highlighting reactions by cofactors
Highlighting by Reaction Name or Frame Id
Highlighting Reactions by Enzyme Name
Highlighting by Reaction EC Number
Highlighting by Reaction Name Substring
Highlighting by CoFactor Name or Frame Id
Highlighting by CoFactor Substring
Highlighting by CoFactor Structure
Highlighting by Activator Name or Frame Id
Highlighting by Activator Substring
Highlighting by Activator Structure
Highlighting by Inhibitor Name or Frame Id
Highlighting by Inhibitor Substring
Highlighting by Inhibitor Structure
Highlighting Reactions by CCO
Highlight Reactions by Species Comparison
Highlighting Enzyme by Curation
Highlighting Reactions by Evidence
Highlighting From Gene File
Omics Viewer Data and Parameters
Omics Viewer Control Panel
Omics Viewer Quick Help
The Pathway Tools Omics Viewer (formerly the Pathway Tools Expression Viewer) paints
data values from the user's high-throughput and other experiments onto the
Cellular Overview diagram for an organism.
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.
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