Clusters 5.50 for MS-Windows.

Serf Software that makes heatmap analysis easier.

Serf Software Suite

Clusters is a program to manipulate genetic heatmaps for MS-Windows 2000 and up.

The more intensive calculations have been optimised for 4 processor cores.
Clusters accepts ASCII data, and outputs a vector drawing that may be integrated into publication-ready drawing sheets created by other members of the Serf Software Suite.

(contextual) Help is provided in HTML.
Browse the online manual.


The basic idea behind Clusters is to manipulate the expression profiles of thousands of genes graphically rather than to inspect virtually endless columns of numerical data. Clusters is the youngest member of the Serf Software Suite and is likely to grow in capacity and the number of options offered in the near future.Copy your mRNA expression data from, for example a NCBI GEO Profiles page and paste it on Clusters' spreadsheet:

Next, select the entire matrix of data (<ctrl>A), and issue the "make heatmap" command. Alternatively, download the NCBI GEO Profiles soft file and open it in Clusters:

The heatmap will then be created automatically. Once you've created your heatmap, you can remove or select entries according to several criteria: 1) the identifier name. 2) The presence of multiple digits, as some entries have no recognisable gene name, but just a character followed by a number. 3) it's absence in the HUGO gene list, 4) difference in expression. If the mRNA expression does not vary depending on experimental condition, then the gene in question may not be very interesting. 5) The location in the cluster tree. With Clusters cut tool you can disect parts of the heatmap for removal or closer examination. 6) Position in a 3D graph representing the three principal components (PCs).

With one click of the mouse compare gene expression between experimental groups:

In conjunction with Clusters, use ATCG to remove numbers, white space and line feeds from the nucleotide sequence that you've just copied from the internet with one click on your computer's speed bar.

Clusters is amply documented and help is provided in several ways: by key word search, by context and by menu item. The doc file includes a comprehensive step by step tutorial. Under Windows 10, the tutorial can be found by clicking "All applications" in the start menu. Then look for the Clusters folder, which contains Clusters.doc.