<think>
Alright, I'm looking at this query where someone is asking about how pathway enrichment analysis was conducted in a scientific article. They want specific details extracted and organized into a table. The user has provided six questions that need answers based on the article's content.

First, I'll start by understanding each of the questions:

1. What tool was used for pathway enrichment analysis?
2. Was a tool version number provided?
3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)?
4. Was a background gene list defined for pathway enrichment analysis?
5. What statistical test was used for enrichment analysis?
6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?

I need to carefully go through the Methods section and possibly other parts of the article to find these details.

Starting with question 1: The tool used for pathway enrichment analysis. In the Material and Methods section, under "Functional Enrichment Analysis," the article mentions using the R-package piano_1.16.4 for KEGG enrichment analysis. So, the primary tools are R with the piano package and possibly other built-in functions.

Question 2: The version number of the tool. It does mention R-3.4.1 and piano_1.16.4, so yes, versions are provided.

Question 3: Gene set libraries queried. They used KEGG pathways as mentioned in the text. Additionally, they reference GO annotations, so both GO and KEGG are utilized.

Question 4: Background gene list. The article states that the background is the whole set of genes from the Agilent microarray, which serves as the background for analysis.

Question 5: Statistical test used. It mentions Fisher’s exact test for enrichment assessment, specifically in the context of KEGG pathways using the piano package.

Question 6: FDR correction. The article applies Benjamini-Hochberg correction to control multiple testing and false positives, so yes, it's used.

I need to ensure I'm not missing any details from other sections. The Functional Enrichment Analysis part is quite thorough, mentioning both GO and KEGG, the tools like R and piano, the statistical methods, and background definitions.

Putting this all together, each answer should be concise but accurate based on the provided text.
</think>

### Pathway Enrichment Analysis Details:

| **Question**                                         | **Answer**                                                                                                                                                                                                 |
|-----------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| **1. What tool was used for pathway enrichment analysis?** | R-package `piano_1.16.4` and additional tools like the KEGG “User data mapping” tool for generating KEGG pathway plots.                                                                                             |
| **2. Was a tool version number provided?**            | Yes, the versions are specified: `R-3.4.1`, `piano_1.16.4`.                                                                                                                                                   |
| **3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** | Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).                                                                                                                                      |
| **4. Was a background gene list defined for pathway enrichment analysis?** | Yes, the background gene list corresponds to the whole set of genes represented on the Agilent 8 × 60 K Whole Human Genome Oligo Microarray.                                                                                   |
| **5. What statistical test was used for enrichment analysis?** | Fisher’s exact test.                                                                                                                                                                                       |
| **6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** | Yes, Benjamini-Hochberg correction was applied to correct p-values for multiple testing.                                                                                                                         |

Let me know if you'd like further clarification!