Discovering transcriptional modules from motif, chip-chip and microarray data.
We present a method for inference of transcriptional modules from heterogeneous data sources. It allows identifying the responsible set of regulators in combination with their corresponding DNA recognition sites (motifs) and target genes. Our approach distinguishes itself from previous work in literature because it fully exploits the knowledge of three independently acquired data sources: ChIP-chip data; motif information as obtained by phylogenetic shadowing; and gene expression profiles obtained using microarray experiments. Moreover, these three data sources are dealt with in a new and fully integrated manner. By avoiding approaches that take the different data sources into account sequentially or iteratively, the transparency of the method and the interpretability of the results are ensured. Using our method on biological data demonstrated the biological relevance of the inference.
De Bie
Tijl
T
KULeuven, ESAT-SCD, Kasteelpark Arenberg 10, 3001 Leuven, Belgium.
Monsieurs
Pieter
P
Engelen
Kristof
K
De Moor
Bart
B
Cristianini
Nello
N
Marchal
Kathleen
K
D000465:Algorithms; D002453:Cell Cycle / Q000235:genetics; D005656:Fungal Proteins / Q000235:genetics; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D015203:Reproducibility of Results; D012270:Ribosomes / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics*; D014158:Transcription, Genetic
D005656:Fungal Proteins