DNA microarray data and contextual analysis of correlation graphs.
BACKGROUND
DNA microarrays are used to produce large sets of expression measurements from which specific biological information is sought. Their analysis requires efficient and reliable algorithms for dimensional reduction, classification and annotation.


RESULTS
We study networks of co-expressed genes obtained from DNA microarray experiments. The mathematical concept of curvature on graphs is used to group genes or samples into clusters to which relevant gene or sample annotations are automatically assigned. Application to publicly available yeast and human lymphoma data demonstrates the reliability of the method in spite of its simplicity, especially with respect to the small number of parameters involved.


CONCLUSIONS
We provide a method for automatically determining relevant gene clusters among the many genes monitored with microarrays. The automatic annotations and the graphical interface improve the readability of the data. A C++ implementation, called Trixy, is available from http://tagc.univ-mrs.fr/bioinformatics/trixy.html.
Rougemont
Jacques
J
TAGC, INSERM-ERM 206, Parc Scientifique de Luminy Case 906, 13288 Marseille Cedex 09, France. rougemont@tagc.univ-mrs.fr
Hingamp
Pascal
P
D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods* / Q000706:statistics & numerical data; D003196:Computer Graphics / Q000706:statistics & numerical data; D016288:Computer Terminals / Q000706:statistics & numerical data; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D015966:Gene Expression Regulation, Fungal / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D006801:Humans; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000145:classification / Q000235:genetics; D016393:Lymphoma, B-Cell / Q000145:classification / Q000235:genetics; D016403:Lymphoma, Large B-Cell, Diffuse / Q000145:classification / Q000235:genetics; D009716:Numerical Analysis, Computer-Assisted; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software; D009626:Terminology as Topic