Question

Which of the following is untrue about Expression Profiling–Based Method?

(a) Genes with similar expression profiles are considered coexpressed, which can be identified through a clustering approach

(b) This approach appears to be less effective for finding transcription factor binding sites

(c) An advanced alignment-independent profile construction method such as EM and Gibbs motif sampling is often used in finding the subtle sequence motifs

(d) The basis for coexpression is thought to be due to common promoters and regulatory elements

The question was posed to me in an interview.

This key question is from Prediction Algorithms in division Promoter and Regulatory Element Prediction of Bioinformatics

Answer 1

Correct choice is (b) This approach appears to be less effective for finding transcription factor binding sites

The explanation is: This approach is essentially experimentally based and appears to be robust for finding transcription factor binding sites. The problem is that the regulatory elements of coexpressed genes are usually short and weak. Their patterns are difficult to discern using simple multiple sequence alignment approaches.