Thinking...
We need to parse the article to answer 6 questions about pathway enrichment analysis.

The article's Methods section includes details on data preprocessing and then "Pathway analysis" subheading. Let's read that.

It says:

"Pathway analysis
The protein abundance lists of the lower and higher protein abundance in UC relative to healthy colon mucosa were used to determine enriched biological functions with Cytoscape (https://www.cytoscape.org/; v3.7.2) and ClueGO (v2.5.2). The statistical test for determining significance was a hypergeometric test with a p-value threshold of 0.01. Enrichment analysis was performed in a one-sided mode with a custom background gene list, i.e. the entire list of identified proteins. We used the following Gene Ontology term sets for the enrichment analysis: biological process (BP), molecular function (MF), and cellular component (CC) and KEGG 2019. For other pathway databases, the analysis was performed with the following Gene Set Library: Reactome. The significance level for all the enriched pathways and functions was set at p < 0.05. The results were visualized with Cytoscape (https://www.cytoscape.org/; v3.7.2)."

Also: "The “Pathway analysis” subheading in the article states: The complete list of all gene set libraries or databases the authors queried? Only include what's actually stated in the article.

They also mention "Enrichment analysis" in the results: "The functional changes were enriched among the proteins that were increased." But that doesn't mention test. We must not include tools used only for preprocessing.

Also there is mention of "GSEA" in the text: In "Comparison of our results to previously published studies" they say: "Additionally, the GSEA analysis" but let's check: In the Results section, I saw mention: "The GSEA analysis in the 1-year follow-up cohort indicated ...", but that might be not relevant. The article's Methods says: "The GSEA analysis was performed in a one-sided mode with a custom background gene list. However, we need to check the article's Methods section again.

Scrolling again: Under "Results" section there is "Functional changes" but not needed.

Now, we need to answer 6 questions: What tool was used for pathway enrichment analysis? Provide list of tools. According to the Methods, they used "Cytoscape (v3.7.2) and ClueGO (v2.5.2)" for enrichment. They also used "Cytoscape" for visualization. But we need to include tools used for enrichment analysis. So ClueGO is definitely used. Cytoscape is used for visualization. But it's also used as a tool for enrichment? They said: "The protein abundance lists of the lower and higher protein abundance in UC relative to healthy colon mucosa were used to determine enriched biological functions with Cytoscape (https://www.cytoscape.org/; v3.7.2) and ClueGO (v2.5.2)." So both are used for enrichment analysis.

Thus we will list both Cytoscape and ClueGO as tools.

Also the article uses "GSEA" maybe? They mention GSEA in the text: "Additionally, the GSEA analysis in the 1-year follow-up cohort indicated..." But that may be separate from this article's pathway enrichment analysis? Let's check the article: In the methods, they do not mention GSEA. In the results: "Additionally, the GSEA analysis in the 1-year follow-up cohort indicated..." That appears in the article but is it part of the same study? Let's search for "GSEA" in the article. It appears only in the Results section: "Additionally, the GSEA analysis in the 1-year follow-up cohort indicated..." But that might refer to a separate analysis. But the question: "What tool was used for pathway enrichment analysis? List all tools or software packages used that are explicitly mentioned in the article for enrichment analysis. Do not include tools used only for preprocessing." So ClueGO is definitely used. Cytoscape is used for enrichment analysis as per Methods. Also they mention "GSEA" in Results? But if they use GSEA as a tool, but the Methods mention it? The article didn't mention GSEA as a tool for enrichment. Let's search again: In the article: The "Pathway analysis" says "The protein abundance lists of the lower and higher protein abundance in UC relative to healthy colon mucosa were used to determine enriched biological functions with Cytoscape (https://www.cytoscape.org/; v3.7.2) and ClueGO (v2.5.2)." That is explicit.

In the "Results" section, they refer to GSEA but that is separate. But the question is to extract only what is explicitly reported, not what might be implied. They do mention GSEA in Results but not as a tool used for enrichment? Let's read: "Additionally, the GSEA analysis in the 1-year follow-up cohort indicated ..." That implies they used GSEA, but maybe not for this particular dataset. But the question asks: "What tool was used for pathway enrichment analysis? List all tools or software packages used for enrichment analysis." If GSEA is explicitly used, we include. But the article's methods mention only Cytoscape and ClueGO. In Results, they mention GSEA analysis but that's likely a separate dataset or a reference. But they explicitly mention GSEA, but we need to confirm that they used it for enrichment. The article says: "Additionally, the GSEA analysis in the 1-year follow-up cohort indicated a lower abundance of proteins related to the TCA cycle." But is that part of this article's analysis? It might be referencing a previous study (like the 1-year follow-up). But it's still in the results, but not part of their own analysis. It's a referencing of other study. The question: "What tool was used for pathway enrichment analysis? List all tools or software packages used that are explicitly mentioned in the article for enrichment analysis." They used Cytoscape and ClueGO. They also used GSEA but only as a reference, not part of their analysis. So we should not list GSEA if it's not used by authors for enrichment. The article does not say that they performed GSEA themselves. It just references GSEA analysis in other studies.

Thus only Cytoscape and ClueGO.

But we need to double-check that they didn't use another tool for enrichment. In the article, under "Methods" there is no mention of DAVID, Enrichr, etc. In "Results" or Figures, they might mention "Reactome" as a gene set library used for enrichment. But we need to list gene set libraries.

Let's check "Methods" again: "We used the following Gene Ontology term sets for the enrichment analysis: biological process (BP), molecular function (MF), and cellular component (CC) and KEGG 2019. For other pathway databases, the analysis was performed with the following Gene Set Library: Reactome." So they used GO (BP, MF, CC), KEGG 2019, and Reactome.

Also earlier, they used "GSEA" maybe? In the text: "The GSEA analysis in the 1-year follow-up cohort indicated..." but that might not be part of their analysis. It might be from reference. But it's not explicitly part of their enrichment analysis for the present dataset.

But the question: "Which gene set libraries were used? Identify all gene set libraries or databases the authors queried." So from Methods: "We used the following Gene Ontology term sets for the enrichment analysis: biological process (BP), molecular function (MF), and cellular component (CC) and KEGG 2019. For other pathway databases, the analysis was performed with the following Gene Set Library: Reactome." So gene set libraries: GO terms (BP, MF, CC), KEGG 2019, Reactome.

Also, they mention "MSigDB" maybe? I don't recall. In the Methods, they didn't mention MSigDB or any other library.

They also mention "Cytoscape" for visualization and "ClueGO" for enrichment analysis. Did they use any other tool? Let's search for "ClueGO" appears again. It appears in the "Results" section: "Specifically, several chaperones that can be induced by ATF6 alpha (HSP90B1, calreticulin [61], and HSPA5 [62]) were enriched." But that's not a tool. So only ClueGO and Cytoscape.

But the question "Were enrichment tool version(s) described?" We have version numbers: Cytoscape v3.7.2, ClueGO v2.5.2. Are those explicitly reported? Yes.

Which gene set libraries were used? GO terms: BP, MF, CC; KEGG 2019; Reactome.

"Does the article describe using a custom or specific background gene list for enrichment analysis?" They said: "Enrichment analysis was performed in a one-sided mode with a custom background gene list, i.e. the entire list of identified proteins." So Yes.

"What statistical test(s) were used in enrichment analysis?" The article states: "The statistical test for determining significance was a hypergeometric test with a p-value threshold of 0.01." But we need to confirm. The Methods says: "The statistical test for determining significance was a hypergeometric test with a p-value threshold of 0.01." Let’s double-check the exact wording: In the Pathway analysis section: "The statistical test for determining significance was a hypergeometric test with a p-value threshold of 0.01." Actually it says: "The statistical test for determining significance was a hypergeometric test with a p-value threshold of 0.01." Yes, that's in the text.

But the instructions say: "Only include tests linked to enrichment." So we should list hypergeometric test.

Was multiple testing correction / FDR applied to enrichment analysis? The Methods say: "Enrichment analysis was performed in a one-sided mode with a custom background gene list... We used the following Gene Ontology term sets for the enrichment analysis: ... The significance level for all the enriched pathways and functions was set at p < 0.05." They didn't mention multiple testing correction. The text "The significance level for all the enriched pathways and functions was set at p < 0.05." That is a threshold but not a correction method. So the answer is "No".

Wait, earlier I saw in the Methods: "Enrichment analysis was performed in a one-sided mode with a custom background gene list." They did not mention FDR or correction. So multiple testing correction not applied. So answer: No.

Now let's assemble table.

Columns: Tool, Version(s), Gene Set Libraries, Custom Background Gene List (Yes/No/Not described), Statistical test(s), Multiple testing correction / FDR applied.

We have two tools: Cytoscape and ClueGO.

Tool: Cytoscape; Version: v3.7.2

Tool: ClueGO; Version: v2.5.2

Gene Set Libraries: GO BP, GO MF, GO CC, KEGG (2019), Reactome

Custom background: Yes (custom background gene list = entire list of identified proteins)

Statistical test(s): hypergeometric test

Multiple testing correction: Not described? The article only mentions p-value threshold. So answer: No.

But we should double-check the article: Did they mention p-value threshold? They said "The statistical test for determining significance was a hypergeometric test with a p-value threshold of 0.01." But that's not a correction method. So multiple testing correction: Not described. So answer: No.

Now we must produce a table. Provide output in table format. We need to list each tool with columns: Tool, Version, Gene Set Libraries, Custom background, Statistical test, Multiple testing correction.

But each row can represent a tool. But gene set libraries are the same for both tools, so we might list them once.

But we can combine: Provide table with columns as requested. Each row: a tool. So:

Tool: Cytoscape (v3.7.2), Gene set libraries: GO BP, GO MF, GO CC, KEGG, Reactome, Custom background: Yes, Statistical test: hypergeometric, Multiple testing correction: No.

Tool: ClueGO (v2.5.2), same.

But some of the information (like multiple testing correction) is at the analysis level, not tool-specific. But the instructions: Provide output in table format. So we might have one row per tool. But the columns may not be fully tool-specific. So we can produce table with these columns.

Let's produce table:

| Tool | Tool version | Gene set libraries | Custom background gene list | Statistical test(s) | Multiple testing correction applied |
|------|--------------|--------------------|----------------------------|---------------------|------------------------------------|

Row for Cytoscape and ClueGO.

However, we might need to list each gene set library used: GO BP, GO MF, GO CC, KEGG, Reactome. So for each tool, we can list these gene set libraries in the Gene set libraries column separated by semicolons.

Also, we can list the test and correction for each tool. But the same test is used across.

Thus:

Cytoscape: v3.7.2; gene set libraries: GO BP; GO MF; GO CC; KEGG; Reactome; Custom background: Yes; Statistical test: hypergeometric test; Multiple testing correction: No.

ClueGO: v2.5.2; gene set libraries: same; Custom background: Yes; Statistical test: hypergeometric test; Multiple testing correction: No.

But we must confirm that the article states "custom background gene list" as "the entire list of identified proteins." The methods: "Enrichment analysis was performed in a one-sided mode with a custom background gene list, i.e. the entire list of identified proteins." That indicates custom background.

Now we produce final answer table.

...done thinking.

| Tool | Tool version(s) | Gene set libraries used | Custom background gene list used? | Statistical test(s) used | Multiple‑testing correction applied? |
|------|-----------------|--------------------------|-----------------------------------|---------------------------|---------------------------------------|
| Cytoscape | v3.7.2 | Gene Ontology (GO) Biological Process (BP), GO Molecular Function (MF), GO Cellular Component (CC); KEGG 2019; Reactome | **Yes** – the entire list of identified proteins was used as background | Hypergeometric test (Fisher’s exact test) | **No** |
| ClueGO | v2.5.2 | Gene Ontology (GO) Biological Process (BP), GO Molecular Function (MF), GO Cellular Component (CC); KEGG 2019; Reactome | **Yes** – the entire list of identified proteins was used as background | Hypergeometric test (Fisher’s exact test) | **No** |