Category Cross-Omics>Pathway Knowledge Bases/Databases/Tools and Genomics>Gene Expression Analysis/Profiling

Abstract PATIKAmad (PATIKA - Pathway Analysis Tools for Integration and Knowledge Acquisition) is a comprehensive microarray data analysis component of PATIKAweb (see G6G Abstract Number 20268), integrated into PATIKAweb's advanced visualization environment.

The tool enables users to visualize microarray data mapped onto pathway models.

It also provides mechanisms for clustering microarray data using popular methods.

PATIKAmad features/capabilities include:

Loading Data -- PATIKAmad offers a native expression data file format (.pmad) and supports the conversion of tab-delimited data files into this format.

This file format is an XML-based format containing information about the experiments (description and values to be analyzed).

Previously created pmad files can be directly loaded into PATIKAmad.

After being loaded, all visualized objects are associated with the first experiment in the loaded data file.

For instance, as the pathway models change on new queries, the loaded data is associated to any newly introduced objects whenever possible.

Visualization of Microarray Data on Pathways -- In PATIKAmad it is possible to map microarray data onto bioentities in a 'bioentity view' and simple states in a 'mechanistic view'.

This mapping can be visualized by color-coding and/or labeling the view objects.

Configuring Visualization Settings -- Visualization options for microarray data can be configured using the "View Settings Dialog" feature in PATIKAmad.

You can specify any number of colors and corresponding values for the desired color-coding.

Then, in-between values are displayed with in-between colors, which have been computed accordingly. Optionally, values can be displayed on related 'pathway view objects' as labels.

Microarray Data Management -- When multiple experiments are loaded into PATIKAmad, the user may choose which group of experiments to be averaged or which two (2) groups of experiments are to be compared.

This is done by using the "Microarray Data Management Dialog" feature.

Querying with Values Table -- The Values Table displays the rows of the loaded microarray data. This table color-codes the experiments to be averaged and/or compared.

A separate column is used to show the calculated values that are displayed on the graph. It is possible to sort the values on this table according to the values and/or filter rows, according to their references.

Graph-of-Interest Query using Significant Microarray Values -- A graph- of-interest query may be used for discovering links between significantly expressed (or differentially expressed) nodes.

The user needs to state their criteria of significance, limit of path length between nodes to search, and the type of graph result requested. Cluster Analysis / Filtering, Normalizing and Clustering Microarray Data /

Cluster Visualization --

The purpose of microarray cluster analysis is to group genes on the basis of similarity/dissimilarity of their expression profiles.

As microarray experiments get more widely used, they become more and more dependent on cluster analysis and other biostatisticial methods since it is almost impossible to make sense of expression profiles of thousands of genes manually.

Cluster analysis of microarray data has already demonstrated great potential for disease identification, finding genes responsible for specific diseases and drug discovery.

PATIKAmad is unique in its integrated tools to perform cluster analysis and visualize the results as partitioned pathways.

A step-by-step illustration of performing cluster analysis and visualizing its results as a pathway is available as part of the documentation of PATIKAmad.

System Requirements

PATIKAmad is a component of PATIKAweb version 2.1, which is publicly available for non-profit use, and the implementation uses the JSP (JavaServer Pages technology) edition of the 'Tom Sawyer Visualization' technology to handle this highly-dynamic and advanced visual content.


Manufacturer Web Site PATIKAmad

Price Contact manufacturer.

G6G Abstract Number 20269

G6G Manufacturer Number 100408