Predicting condition specific transcription factors for target gene. - - PowerPoint PPT Presentation

Predicting condition specific transcription factors for target gene.

Kaur Alasoo 19.09.2012

Target gene Factor 1 Factor 2 Factor 3 Factor 4 Factor 1 Factor 2

Baseline Stress 1 Stress 2

• ArrayExpress

Differential expression was calculated in 234 manually curated yeast gene ex- pression data sets from ArrayExpress leading to 1464 pairwise comparisons.

YEASTRACT database

Known targets of 184 TFs [1].

Disruptome

Analyzed expression data from 269 yeast TF knock-out strains [2].

TRAP

Predicted binding affinities of all TFs to the target promoter sequence from Transcription Factor Affinity Prediction tool (TRAP) [3].

TF1 TF2 TF3 Gene 1 Gene 3 Gene 5 Gene 9 TPO1 Gene 2 Gene 4 Gene 6 Gene 7 Gene 8

Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Gene 6 Gene 7 Gene 8 Gene 9 TPO1 Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Gene 6 Gene 7 Gene 8 Gene 9 TPO1 Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Gene 6 Gene 7 Gene 8 Gene 9 TPO1 1 2 3 1 2 3 4 5 6 7 8 9 10

Comparisons Differential expression rank

TF1 TF2 TF3 TF2 TF3 TF1 TF2 TF3 TF1 1 2 3 1 2 3

Gene Set Analysis

TF2 TF3 TF1 1 2 3

Rank Aggregation

Ranked list of TFs

TF1 TF4 TF5 TF6 TF7 TF3 TF8 TF9 TF10 TF2 1 2 3 4 5 6 7 8 9 10

Ranked list of TFs

TF9 TF10 TF6 TF4 TF1 TF3 TF8 TF7 TF5 TF2

Ranked list of TFs

1 2 3 4 5 6 7 8 9 10

p-value p-value score

Final rank aggregation

• wild type vs. mutant

water vs. ethanol ...