Pathway Tools Cellular Overview

Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools and Cross-Omics>Pathway Knowledge Bases/Databases/Tools

Abstract The Pathway Tools Cellular Overview diagram is a visual representation of the biochemical network of an organism.

The overview is automatically created from a Pathway/Genome Database (PGDB) describing that organism.

The cellular overview includes metabolic, transport and signaling pathways, and other membrane and periplasmic proteins. Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram.

Furthermore, a software component called the Omics Viewer - (see G6G Abstract Number 20237), provides visual analysis of whole-organism datasets using the overview diagram as an organizing framework.

For example, gene expression and metabolomics measurements, alone or in combination, can be painted onto the overview, as can computed whole-organism datasets, such as predicted reaction-flux values.

The Cellular Overview and Omics Viewer provide a mechanism whereby biologists can apply the pattern-recognition capabilities of the human visual system to analyze large-scale datasets in a biologically meaningful context.

SRI’s website - (see G6G Abstract Number 20230), provides “overview diagrams” for more than 200 organisms.

System-level visualization of metabolic networks --

Pathway Tools can automatically generate organism-specific metabolic charts that are called Cellular Overview diagrams (as stated above...).

The diagram can be generated as a graphic, on the computer screen, that can be interrogated interactively and used to analyze omics datasets. It can be generated as a PDF file for printing as a large-format poster.

For example an entire diagram (Not shown here...) at low resolution can be painted with gene expression data. It can contain all known metabolic pathways and transporters of an organism.

Each node in the diagram can represent a single metabolite, and each line can represent a single bioreaction.

Omics data (e.g. gene expression or metabolomics measurements) for a given organism can be painted onto the cellular overview to place these data in a pathway context and to allow the user to discern the coordinated expression of entire pathways [such as the tricarboxylic acid (TCA) cycle], or of important steps within a pathway.

Omics data may be loaded from a data file and superimposed on the Overview diagram for that organism.

Cellular Overview diagrams generated automatically --

Cellular Overview diagrams are generated automatically using an advanced layout algorithm.

Automated layout is essential to allow the diagram to accurately depict the underlying database (DB) content as that content evolves, without requiring time-consuming manual updates by curators that are bound to overlook some updates.

In addition, automated layout allows generation of organism-specific cellular overviews that reflect the exact pathway content of each organism-specific PGDB in large PGDB collections such as BioCyc.

Cellular Overview capabilities --

The Cellular Overview in the desktop version of Pathway Tools has many capabilities.

These capabilities include:

1) Semantic zooming of the diagram;

2) Highlighting of user-requested elements of the diagram (such as metabolites or pathways);

3) Highlighting large biologically relevant subnetworks (such as all reactions regulated by a given transcription factor, and the results of a reachability analysis); and

4) Highlighting comparative analysis results such as comparison of the metabolic networks of two (2) or more PGDBs.

Note: The desktop version of Pathway Tools that you can install locally provides different and additional operations then the Web Cellular Overview and vice-versa.

Cellular Overview Diagram --

The Cellular Overview diagram depicts the biochemical machinery of an organism as described in a PGDB. Each node in the diagram (such as the small circles and triangles) represents a single metabolite, and each blue line represents a single bioreaction.

Different PGDBs will have different components of the diagram present or absent depending on what was included by the PGDB authors.

Organization of the Cellular Overview --

Within the cytoplasmic membrane, the small-molecule metabolism of the organism is depicted in several regions.

The glycolysis and the TCA cycle pathways, if present, will be placed in the middle of the diagram to separate predominately catabolic pathways on the right from pathways of anabolism and intermediary metabolism on the left.

The existence of anaplerotic pathways prevents rigid classification. The majority of pathways operate in the downward direction.

Signal transduction pathways, if present, run along the bottom of the diagram. Pathways are grouped into related clusters as indicated by the shaded regions.

The large group of individual reactions at the right of the diagram represent, reactions of small-molecule metabolism that have Not been assigned to any pathway.

The shapes of the metabolite icons represent various compound classes. The different shapes used are as follows:

1) Triangle: Amino Acids;

2) Square: Carbohydrates and Derivatives;

3) Diamond: Proteins and Modified Proteins;

4) Vertical Ellipse: Purines;

5) Horizontal Ellipse: Pyrimidines;

6) T: tRNAs;

7) Circle: All other compounds; and

8) Filled shape: Phosphorylated compound.

The one or more cellular membranes of the organism are depicted, depending on the cellular architecture of the organism, and on whether that architecture was specified when the PGDB was created.

Transporters will be depicted in the membrane in which they reside as blue lines whose arrowhead indicates the direction of transport. For gram-negative bacteria, periplasmic proteins will be depicted when identified in the PGDB.

System Requirements

The Cellular Overview has been tested on Internet Explorer 8.0, Firefox 3.5, Safari 4.0 and Chrome 2.0.

It is recommended by the manufacturers Not to use Internet Explorer for the Cellular Overview process since its performance can be very poor.

The performance of the three (3) other browsers are much better compared to Internet Explorer.

Contact manufacturer for further details.


Manufacturer Web Site Pathway Tools Cellular Overview

Price Contact manufacturer.

G6G Abstract Number 20189A

G6G Manufacturer Number 102506