Thinking...
We need to extract explicit details about pathway enrichment analysis from Methods, Results, etc.

We have to answer 6 questions:

1. What tool was used for pathway enrichment analysis? List all tools or software packages used for enrichment analysis.

2. Were enrichment tool version(s) described? Provide version numbers associated.

3. Which gene set libraries were used? Identify all gene set libraries or databases queried.

4. Does the article describe using a custom or specific background gene list for enrichment analysis? Options Yes/No/Not described.

5. What statistical test(s) were used in enrichment analysis? Name of tests.

6. Was multiple testing correction / FDR applied to enrichment analysis? Only yes if explicitly mentioned.

We need to examine Methods section, but also results.

From the article:

In "DMRs and DMGs Identify" section:

"EdgeR integrated in the R packages MEDIPS with..." etc.

But not relevant.

Then: "Further, ChIPseeker was performed to annotate the DMRs in gene level, and only the genes with promoter annotated by DMRs were defined as differential methylated genes (DMGs) ([139]Yu et al., 2015). All DMGs were subsequently analyzed with GO and KEGG pathway of the DAVID web server ([140]Huang da et al., 2009)."

Thus pathway enrichment analysis: they used DAVID web server.

They used GO and KEGG pathway for enrichment.

Also earlier in "Analysis of MeDIP-Seq Data" they mention MACS for peak distribution.

But for enrichment: The article says: "All DMGs were subsequently analyzed with GO and KEGG pathway of the DAVID web server ([140]Huang da et al., 2009)."

Thus tool: DAVID.

Version not described: maybe not; the reference indicates using the DAVID web server (Huang et al., 2009). No version number provided.

Gene set libraries: GO and KEGG.

Custom background gene list: Not described? They said "All DMGs were subsequently analyzed with GO and KEGG pathway of the DAVID web server". No mention of custom background gene list. Probably not described.

Statistical test: Typically DAVID uses Fisher's exact test or hypergeometric test. But the article doesn't state which test used. It just says "DAVID web server". We need to look at Results or figure legends for mention of test.

In Results: "The 202 overlap genes were identified by comparing DMGs and DEGs. Most of the genes were related to satellite cell function and muscle development, including positive regulation of cell migration, positive regulation of smooth muscle cell proliferation, Wnt signaling pathway, calcium modulating pathway, and regulation of cell proliferation. Cluster analysis revealed that many of the overlap genes had a lower methylation levels at Week 2." They didn't mention statistical test. In figure legend: "Not described".

In "Analysis of MeDIP-Seq Data": They used MACS.

In "DMRs and DMGs Identify": "EdgeR integrated in the R packages MEDIPS with...".

But no mention of enrichment test.

They used DAVID web server but didn't mention multiple testing correction.

In "Results" they refer to "significantly enriched" for Wnt signaling pathway.

But not the statistical test.

Thus we answer:

Tool: DAVID.

Version: Not described.

Gene set libraries: GO, KEGG.

Custom background: Not described.

Statistical test: Not described.

Multiple testing correction: Not described.

We need to present table format.

Let's confirm no other tool: In "Materials and Methods" they used "ChIPseeker" to annotate DMRs. But that's annotation not enrichment.

Also "DAVID" is only enrichment tool used.

Thus answer.

Now produce table.

But check the article again: In "Materials and Methods" section: There's a subsection "Analysis of MeDIP-Seq Data" and "DMRs and DMGs Identify" where they mention "All DMGs were subsequently analyzed with GO and KEGG pathway of the DAVID web server ([140]Huang da et al., 2009)."

Thus confirm.

They didn't describe version numbers.

So output:

| Question | Answer(s) |
We need to create table with 6 columns: "Tool used for pathway enrichment analysis", "Enrichment tool version(s)", "Gene set libraries used", "Custom/background gene list used?", "Statistical test(s) used", "Multiple testing correction/FDR applied".

But the first column: "What tool was used for pathway enrichment analysis?" So we put "DAVID" (only tool). For multiple tools, list separately; but only one.

Second column: "Were enrichment tool version(s) described?" Provide version numbers associated; but not reported => Not described.

Third column: "Which gene set libraries were used?" Identify all gene set libraries or databases authors queried; only actually stated: GO, KEGG. Also maybe "GO" and "KEGG" as part of DAVID. The article may also mention "DAVID web server" but not gene set libraries; but they used GO and KEGG.

Fourth column: "Does the article describe using a custom or specific background gene list for enrichment analysis?" Options Yes/No/Not described. They didn't mention custom background; so "No".

But let's check: maybe they used default background; but they didn't describe; so "Not described" if not stated. But the options include Yes, No, Not described. We can choose "No" because they didn't describe using a custom or specific background gene list. But we might need to interpret: they didn't say they used custom background; but they may have used default background. The question: "Does the article describe using a custom or specific background gene list for enrichment analysis? Your options include Yes, No or Not described." So if they didn't mention custom background, answer "No" (implied not used). But to be safe, if not described, we could answer "No". The phrasing "custom or specific background gene list" indicates if they mention they used one. They didn't; so "No".

Fifth column: "What statistical test(s) were used in enrichment analysis?" The article didn't mention any. So "Not described".

Sixth column: "Was multiple testing correction / FDR applied to enrichment analysis?" They didn't mention; they only mention p-value threshold maybe; but not FDR. So "No".

But we need to check if anywhere in article they mention FDR threshold for enrichment: In results, "Significantly enriched" might be based on FDR < 0.05? But not explicitly mention. They mention p-value threshold in some analyses? Not sure. They didn't mention FDR for enrichment. So answer "No".

Thus table:

| Tool | Version | Gene set libraries | Custom background? | Statistical test | Multiple testing correction |

But we must list all tools separately. Since only tool is DAVID, we have one row: but table can have columns; maybe multiple rows if multiple tools; but we can just have one row.

However the question: "Provide output in table format." So we need to produce a table with rows: Tool, Version(s), Gene set libraries, Custom background, Statistical test(s), Multiple testing correction.

So table with single row for "DAVID". Let's fill accordingly.

Also for version: "Not described".

Gene set libraries: GO, KEGG.

Custom background: No.

Statistical tests: Not described.

Multiple testing correction: No.

But need to answer as table.

Thus final answer:

| Tool | Version | Gene set libraries | Custom background | Statistical test(s) | Multiple testing correction |

Row: DAVID | Not described | GO, KEGG | No | Not described | No

But we need to fill each column accordingly.

Let's produce table accordingly.
...done thinking.

| Tool used for pathway enrichment analysis | Enrichment tool version(s) | Gene set libraries used | Custom or specific background gene list used? | Statistical test(s) used in enrichment analysis | Multiple testing correction / FDR applied to enrichment analysis |
|-------------------------------------------|---------------------------|------------------------|----------------------------------------------|-----------------------------------------------|------------------------------------------------------------|
| DAVID | Not described | GO, KEGG | No | Not described | No |