Plant Biology
 Department of Biology
 University of Fribourg
 Unifr    Faculty of Science

FiRe and associated macros Homepage


    Please check that you are using the latest version of FiRe. The current version is 2.2

  1. Overview
    1. The FiRe macro
    2. The CompareLists and CompareThreeLists macros
    3. The MergeLists macro
    4. The "Add an html link" macro
    5. The "Draw Heat Maps" macros
    6. Redundant items in Excel tables
    7. Documentation
  2. Requirements and compatibility issues
  3. Conditions of Availability
  4. Version History
  5. Installation
  6. Download
  7. Detailed Instructions
  8. How to cite
  9. Bugs and Features Request


Overview

The FiRe macro

FiRe (for Find Regulons) is an Excel® macro that was designed to quickly survey microarray data by establishing lists of "interesting" candidate genes that follow a given pattern of mRNA accumulation. Genes are selected depending on their fold-change ratios over different experimental conditions. Microarray data from any organism or tissue can be used.

In a first step, the microarray data from different experiments are grouped into a single Excel table. All you have to do is put your data into Excel® spreadsheets, and then, at the request of the macro, locate them by clicking on the first probe/gene of the table.


CreateDataSheet


Then a new spreadsheet will be generated, containing expression ratios (tested conditions compared to the respective control conditions) and their associated "numerical qualifiers" ("1" for ratios greater than the upper threshold, "-1" for ratios lesser than the lower threshold, "0" for ratios between the two thresholds).

MainSheet


The macro allows the selection of genes that present an expression ratio higher or lower than user-defined thresholds in a very intuitive way using the numerical qualifiers.

mainsheetselect


Upper and lower thresholds can be set independantly for each experiment.
ChangeThresholds


FiRe has been designed so that users are free to add personnal annotations on the"Data" and "Main" sheets (eventually using the MergeLists macro). You do not have to pay attention that probes are in column 1, values in column 2, etc.

MainsheetComments


The "Count Regulons" button allows to get a quick idea on the frequency of expression patterns.

CountRegulons


The CompareLists and CompareThreeLists macros

These macros can compare lists of probes, genes or whatever you can make a list of. Defining a list is easy, you only have to click on the top item. Alternatively, a list can be constituted by selecting a range containing the items (when needed this range can be discontinuous). The macro will output the sets of unique and shared items.

CompareThreeLists

Another useful application of these macros is the identification of redundant items within a list. If desired, the macros will output a modified list containing each item only once, and mention its number of repetitions in the original list.

RedundantList

The MergeLists macro

This thoughtfully named macro can merge two Excel® tables into a single one. Several columns from the "source" table can be imported at once into the "target" table.

MergeLists


The MergeLists macro can also be used to "extract" data from a source table only for selected entries.

Extract


Finally, this macro makes it possible to identify and count redundant items in a table. If desired, the macro can output a modified table that lists all the redundant entries at the top of the table, along with their associated data.

RedundantTable


The "Add an html link" macro

Ever gone crazy from manually querying a web-based database with all these gene names? Then this macro is for you! It will automatically link each member of a list to its entry in the database of your choice! By default are included some links useful for the Arabidopsis community.

AddLink

The "Draw Heat Maps" macros

These macros will dramatically improve the readability of  your data by adding a colour code to your rows and columns of figures, thus creating a nice so-called "heat map". Two slightly different macros are available: one will colourize ratios, and the other will process absolute values.

HeatMapRatio


The colours of the colour scales can be changed in a snap. The documentation also details potential pitfalls and issues when using colours in Excel.

ChangeColors

Redundant items in Excel tables

Use the CompareLists and MergeLists macros to identify, count and/or remove redundant items (duplicates, triplicates, etc.) from Excel tables.

Documentation

A nifty documentation for FiRe and associated macros is available and includes a detailed description of the macros, how to use them, and even a troubleshooting section. Plus, you will find an "Excel tips" section that will explain you for instance how to import an Excel® heatmap table into a nice presentation, or how to perform some basic text manipulations (for example: How to extract "At1g01010" from "At1g01010.1" ?)


Requirements and compatibility issues

FiRe and its associated macros only rely on Excel 97® or later. This means that provided that Excel® is installed and functional on your computer, these macros should perform well, no matter whether your machine is PC or Mac. However, we have found that the execution of Excel® macros is quite slow on Macs compared to PCs. We therefore highly recommend that you work on PC if you plan to analyze large sets of data. Obviously, although the macros were optimized for a high-speed execution, it is also preferable to use a recent and fast computer to cut down processing time.

Conditions of Availability

FiRe is free.

The use of FiRe and its associated macros is conditional upon the acceptance of the copyright delivered with FiRe. This copyright can be accessed by clicking on the "Copyright" button on the sheet with all the other macros.


Version History

The current version is 2.2. Earlier versions are not available. Versions earlier than 2.0 were not publicly distributed.

Changes since v2.0:

07/13/2006 v2.2

* fixed: a minor bug caused an temporary worksheet to remain visible instead of being deleted when cancelling a test reaction.
* allowed addition of user data (annotations, p-values, etc.) on the "Data" sheet.
* The "Data" sheet now indicates how many IDs and experiments are stored in the table.
* added a button to run the "Add HTML link" macro on the "Links" worksheet.
* messages emitted by FiRe are now more informative about worksheets newly created.


04/28/2006 v2.01

* fixed: When using MergeLists, the macro would unexpectedly stop if the SourceTable had no header row.

Installation

Since FiRe and its associated macros are distributed as a regular Excel® file, you do not need to install anything. Simply open the file within Excel®.


Download

The latest version of FiRe and its associated macros can be downloaded here.

FiRe users should be aware of this warning about very specific gene names and identifiers in Excel®.

Detailed Instructions

All information you need about FiRe and its associated macros are available as a PDF file. You can download it here.


How to cite

We kindly request that those who used FiRe and/or its associated macros for their published work should cite:

Garcion C., ApplimathFRI & Mˆ©traux J.-P. (2006) Trends in Plant Science 11: 320-322.

Bugs and Features Request

I would find useful to have an extra feature in FiRe or in the associated macros. Will you implement it?
The progenitor of FiRe is currently busy in the lab with "wet" experiments, so unless your request is *very* interesting, chances are low. Still, you can ask for it kindly (Christophe.Garcion_at_unifr.ch) , one never knows...

I found a bug in FiRe. Where can I report it?
Send us an email, along with the minimal set of data that reproduces the bug, and a brief description of your system (PC/Mac, Excel version that demonstrates the bug). If we can reproduce that bug, we will make our possible to correct it.