Client:
A leading life sciences research organization
Challenge:
Identification and analysis of differentially expressed gene data from an information repository of four different plant species, posed a bottleneck in the customer's research.
Strand’s Solution:
- Each experiment in the above analysis has 3 to 4 technical replicates. In our quality check we found that all the samples had a correlation > 0.9 with other technical replicates. Thus, none of the samples were discarded from our analysis.
- Intra-species comparisons between stress and control have higher correlation than inter-species comparisons for the same experimental condition.
- Created several significant gene lists with different corrected p-value cut-offs. We also created alternative significant gene lists using a non-corrected p-value.
- Analyzed the overlaps between different species subjected to the same stress condition. We identified genes that were differentially expressed in the significance analysis of stress versus control across species.
- We subjected the signifcant gene-lists to GO analysis and obtained relevant enriched GO terms.
- We identified several interesting pathways in the analysis. Among these, the auxin signaling pathway appeared relevant to the experiment.