Self-Organizing Map and Other Clustering Methods in Transcriptomics

Abstract

Self-organizing map (SOM) is an artificial neural network algorithm, having been used frequently with transcriptomic data analysis, in particular for clustering co-expressed genes as a basis to infer co-regulated genes. It can be applied to any set of objects as long as a distance function can be defined between objects. SOM is numerically illustrated together with a simple UPGMA method to contrast between the two. A less known application of SOM is in discovering heterogeneous motifs present in a set of sequences, making it more general than Gibbs sampler in de novo motif discovery. These two approaches, one with a (gene × expression) matrix as input and the other with a set of sequences as input (where each sequence may contain multiple but heterogeneous protein-binding sites), are illustrated.

Postscript

A researcher compiles demographic, political, economic, and educational data from many countries in the world and used clustering algorithms and self-organizing map to analyze them. Almost all affluent western countries were mapped to a few closely spaced nodes whereas all poor countries were scattered all over the place.

“All happy families are alike; each unhappy family is unhappy in its own way.” The researcher concluded his presentation with a quote from Leo Tolstoy, highlighting the sharing of democracy among the affluent western countries.

I was impressed, but then the ensuing discussion became disturbing, at least to me, when someone expressed the perhaps noble wish that “It would be so nice if all those poor countries embrace democracy and live like us.”

Spreading democracy and changing regimes have been used as a pretext for wars in recent years, often resulting in millions of homeless refugees.

Have we really developed a social system that can be grafted onto another country and spawn prosperity and happiness?

We as scientists often do our research in different ways, although we all believe in the general principle of scientific method. I surely would pay attention to how successful scientists conduct their research and imitate what they do if it benefits my own research, but I would be appalled if someone walks into my laboratory and demands that I have to do research in his or her way.

Human history has witnessed many wars that erupted because some people thought that they had gained a religion better than others. There are still fundamentalists who believe that the world will become heaven if everyone embraces their extreme views.

During the Great Cultural Revolution in China in late 1960s, young red guards heard, mistakenly, that serfdom was still practiced in Tibet and that the ruling monks maintained such serfdom by brainwashing the believers. Committing themselves to the noble cause of liberating the poor Tibetans, many red guards braved themselves against all the odds to march thousands of miles of treacherous terrains to Tibet. Many young boys and girls died along the way, taking their last breath to bid their comrades to continue their unfinished cause. Those who did reach Potala Palace immediately began to do cultural damage that is felt even today.

Plato believed that arrogance is the root cause of all misunderstanding and evil and illustrated his point brilliantly with his famous allegory of the cave. But we still live like the chained prisoners in the cave. We will not make progress unless we realize how ignorant and depraved we are.