The Alternate Transcript Diversity (ATD) project aims at characterising the alternative transcripts of mRNA present in the human genome. Alternative transcripts of mRNA come into existance for three different reasons: variation in transcription start site, splicing and polyadenylation. It has been observed that the expression of alternative transcripts is specific to tissue-type as well as developmental stage. Disruptions in expression of ATs corresponding to a particular cell condition can cause serious illnesses (e.g. cancer, multiple sclerosis, heart failure and neurodegenerative disorders). Among other things the ATD project aims at characterising AT variants specific to tissue-types as well as detecting ..............

Jun 20 18:16

Apriori Revisited

A paper by T. de Bie et al. describes one very stylish application of the Apriori algorithm for detection of transcription regulatory modules. The idea is in the smart statement of the problem, which is the following:

Find the maximal sets of genes that all share at least r common regulators, at least m common motifs, and have pairwise correlation of at least c.

It turns out that the sets of genes of interest naturally satisfy the same properties as the frequent sets in the Apriori algorithm, so it's rather easy to adapt the algorithm for this context.

Jun 18 14:56

An Improved Map of Conserved Regulatory Sites

You might still remember this paper by Harbison et al. that reported some high-quality S.cerevisiae TF binding sites. Well, now there's a followup by Maclsaac et al.. This time the authors used phylogenetic conservation based algorithms (PhyloCon and Converge) to search for binding sites, and reportedly got even better results than before.

Moreover, the authors provide a nice Python package TAMO for performing basic PWM-matching tasks.