High-throughput Biology - From Sequence to Networks 2019 - Integrated Assignment Day 7

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Pathway and Network Analysis Integrated Assignment: Answers to questions and Screenshots

By Veronique Voisin

The results are stored in this folder.

g:Profiler

Question: What is the most significant GO:term? What is the p-value for this GO:term

Answer: extracellular matrix organization

Question: Is this p-value already corrected for multiple testing? What type of correction is used for your current analysis?

Answer: yes, it is already corrected for multiple hypothesis testing. I set the Significance threshold box to “Benjaminin-Hochberg FDR”.

Re-run the analysis with User p-value threshold set to 0.0001.

Question: What has been changed?

Answer: Only the gene-set with adjusted pvalue equal or less than 0.0001 are displayed. The list is reduced compared to the results obtained with the default settings.

Ordered query:

Question: Do you seen any changes in the output in comparison to the analysis of the unordered gene list (PART 2)

Answer Although some terms are similar, their pvalues changed as well as the number of term genes used to calculate the pvalue.

Question What can you conclude about these networks?

Answer The pathways are relevant to the biological model under study. The changes are related to the transformation of the epithelial cells into mesenchymal ones.

REACTOME FI

Pathway enrichment on the whole network.

Question What is the pathway with the lowest (best) FDR?

Answer The pathway with the lowest FDR is Endometrial cancer (K) with an FDR equal to 5.78w-16.

Cluster the network and perform pathway enrichment on the network.

Question How many clusters did the analysis retrieve?

Answer The analysis retrieved 10 clusters named module 0 to module 9.

Question What is the FDR value of the most significant pathway of module 0?

Answer RAF/MAP kinase cascade (first row)

GeneMANIA

Question What is the number of nodes in the CTNBB1 network.

Answer There are 22 nodes.