Regulated process or chance observation?. Divergent transcription. Joern Toedling Huber group November 2007. Divergent transcription. Transcript orientation. Data Collection. S90 samples, treated with Actinomycin D (ActD+); grown on 3 * YPD 3 * YP+Galactose 3 * YPE: YP+Ethanol
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Regulated process or chance observation?
S90 samples, treated with Actinomycin D (ActD+); grown on
3 * YPD
3 * YP+Galactose
3 * YPE: YP+Ethanol
S96 cell cycle ActD+: 45 samples, one taken each 5 min for 220 min (~ 2 iterations of cell cycle)
9 samples, normalized by use of a genomic DNA sample, grown under 3 different growth conditions, one common segmentation and post-processing, results in 5510 transcripts:
1360 pairs of divergent transcripts
672 pairs of convergent transcripts
781 pairs of tandem transcripts
45 samples, normalized by use of a genomic DNA sample, one common segmentation and post-processing, results in 5596 transcripts:
1266 pairs of divergent transcripts
829 pairs of convergent transcripts
847 pairs of tandem transcripts
are divergent transcripts' levels correlated across cell cycle and is this correlation dependant on the closeness of the transcript boundaries
Which correlation coefficient?
sd(X) * sd(Y)
Spearman CC is based on ranks(X) and ranks(Y) instead of X and Y
Interlude: Interpreting Pearson CC = 0.8
Anscombe, Francis J. (1973) Graphs in statistical analysis. American Statistician, 27, 17–21.
investigate ActD+ Cdc28 cell-cycle data
TF binding motif enrichment in found bidirectional promoters
binding of known motifs (annotated in Transfac and SCPD data bases)
discovery of new motifs, using tools such as MEME
consider restriction to those pairs of divergent transcripts whose expression is correlated across the cell-cycle to distinguish functional divergent pairs from those that just appear to be divergent due to compactness of yeast genome
describe functional bidirectional promoters in yeast
describe filtered novel transcripts from bidirectional promoters
look for new and known TF binding motifs upstream of periodic anti-sense transcripts: