Thinking...
We need to answer six questions in a table format:

1. What tool was used for pathway enrichment analysis? List all tools or software packages used for enrichment analysis, explicitly mentioned in the article for enrichment analysis. Not include tools used only for preprocessing.

In Methods, they say: "Functional enrichment analyses were carried out using GSEA version 4.1.1" and "We performed GSEA to test whether ...". In Results, they used GSEA. Also earlier they used "GSEA" for tissue-specific TRM-associated gene sets. They also mention "GSEA enrichment plots" etc.

They also mention "The enrichment plots for the five TRM-related up-regulated gene sets and down-regulated gene sets were significantly enriched at P value < 0.05 and FDR q-value < 0.25". They mention GSEA.

They also mention "Functional enrichment analyses were carried out using GSEA v4.1.1. ... GSEA enrichment plots for the five TRM-related up-regulated gene sets and five down-regulated gene sets." They also mention "GSEA confirmed that all five up-regulated and five down-regulated gene sets were significantly enriched." That's the only tool used for pathway enrichment analysis? Wait they also used "GSEA enrichment plots" but earlier in Methods they mention "Transcriptional profiles of TGF-β-treated T cells were enriched for TRM-related gene signature" and "We performed GSEA to test whether the differentially expressed genes in the TGF-β-treated groups were enriched for tissue-specific TRM cell-associated genes." They also mention "GSEA enrichment plots" etc. So the tool used: GSEA. Any other tool? They also mention "Functional enrichment analyses were carried out using GSEA v4.1.1" and "The GSEA enrichment plots for the five TRM-related up-regulated and down-regulated gene sets." But earlier they also mention "GSEA enrichment plots for the TCM and TEM-related up-regulated gene sets." So GSEA again.

Additionally, earlier in Methods: "Functional enrichment analyses were carried out using GSEA version 4.1.1." But also earlier in the methods, they used "The tissue-specific TRM cell-associated gene sets comprised genes previously identified as either up- or down-regulated in TRM cells from skin, gut, lung, brain, and liver." So they used a custom gene set library? They might be referencing a custom gene set library of TRM genes. That might be considered a custom gene set library. But the question: Which gene set libraries were used? It includes GO, KEGG, Reactome, etc. They used GO for gene ontology, and they used GSEA for enrichment. But they also used "GSEA enrichment plots for the five TRM-related up-regulated and down-regulated gene sets." But those gene sets are custom defined. So gene set libraries: GO, TRM core signature (35 genes). But that might be a custom gene set library. So we must identify all gene set libraries or databases the authors queried. They used GO for functional enrichment (GO terms). They used "GSEA" for gene set enrichment. They also used "GSEA" to test for enrichment of tissue-specific TRM gene sets, presumably from a library of TRM gene sets. They also used "GSEA" for TCM and TEM gene sets as negative controls.

They also used "GSEA enrichment plots for the TCM and TEM-related gene sets" but said that they were not significantly enriched.

In addition, earlier they mention "GSEA confirmed that all five up-regulated and five down-regulated gene sets were significantly (P-value < 0.05) enriched in the DE genes in our TGF-β-treated groups." So yes.

Now we need to answer the six questions:

1. What tool was used for pathway enrichment analysis? List all tools or software packages used (e.g., DAVID, GSEA, Enrichr, etc.) that are explicitly mentioned in the article for enrichment analysis. Not include tools used only for preprocessing.

Answer: GSEA.

2. Were enrichment tool version(s) described? List the version numbers associated with each enrichment tool, if reported.

Answer: GSEA version 4.1.1.

3. Which gene set libraries were used? Identify all gene set libraries or databases the authors queried (e.g., GO, KEGG, Reactome, MSigDB, etc.). Only include what's actually stated in the article. They used GO (Gene Ontology) for functional enrichment. They also used "GSEA" to test enrichment of "tissue-specific TRM-associated gene sets" (custom gene sets). They also used GSEA for "TEM and TCM related gene sets" as negative control. They also used "GSEA" to test "TRM up-regulated gene sets" and "TRM down-regulated gene sets." So gene set libraries: GO. They also used "tissue-specific TRM gene sets" which are custom sets. Also "TRM core signature" from the literature. So gene set libraries: GO (Gene Ontology), custom gene sets (TRM core signature, tissue-specific TRM gene sets, TCM/TEM gene sets).

Also they might mention "MSigDB" somewhere? They didn't mention it. They didn't mention KEGG, Reactome, etc. So only GO. But they used GSEA for enrichment of custom gene sets, not GO. However, GSEA can test any gene sets. They used GSEA to test gene sets of TRM. But GSEA also can use GO, but in this article they used GO for enrichment of the TRM signature? Wait in Results they mention "Transcriptional profiles of TGF-β-treated T cells were enriched for TRM-related gene signature". They performed GSEA to test for tissue-specific TRM gene sets. They also used GSEA to confirm enrichment of TRM up- and down-regulated gene sets. They also used GSEA to test TCM and TEM gene sets as negative controls.

But earlier, they also performed functional enrichment analyses using GSEA v4.1.1 for "Gene Ontology" terms? Actually, reading earlier: "Functional enrichment analyses were carried out using GSEA version 4.1.1. The GSEA enrichment plots for the five TRM-related up-regulated and down-regulated gene sets in the TGF-β-treated group." But earlier, they also performed "Functional enrichment analyses were carried out using GSEA". Wait earlier in Methods: "Transcriptional profiles of TGF-β-treated T cells were enriched for TRM-related gene signature." They also performed "GSEA to test whether the differentially expressed genes in the TGF-β-treated groups were enriched for tissue-specific TRM cell-associated genes." So the only enrichment tool is GSEA. But earlier, they also mention "functional enrichment analyses were carried out using GSEA v4.1.1." That is the tool. Did they also use "GSEA enrichment plots for the five TRM-related up-regulated and down-regulated gene sets"? Yes.

They also mention earlier in Methods: "Transcriptional profiles of TGF-β-treated T cells were enriched for TRM-related gene signature. We found 46–60% of these genes were consistently expressed in a similar manner in our TGF-β-treated groups." They performed a bootstrapping permutation test. So they used "bootstrapping permutation test" for enrichment significance? Wait earlier: "The overlap between the TRM core signature and the full set of differentially expressed genes in all the three treatment comparisons was statistically significant (P < 0.001) in a bootstrapping permutation test (Methods)." That is for overlap significance. That is not a standard enrichment test? But the question: "What statistical test(s) were used in enrichment analysis? State the name(s) of the statistical test(s) used for enrichment analysis (e.g., hypergeometric test, Fisher's exact test). Only include tests linked to enrichment." So the bootstrapping permutation test is used for significance of overlap. This is a test for enrichment. So we include "bootstrapping permutation test." For GSEA, the statistical test is the Kolmogorov–Smirnov-like test? Actually GSEA uses a Kolmogorov-Smirnov-like test to compute the running enrichment score. But they didn't mention the test. They mention "P-value < 0.05 and FDR q-value < 0.25." They didn't specify the test. They mention that GSEA uses "P-value" and "FDR q-value". They did not explicitly mention the test used in GSEA. They didn't mention "Kolmogorov–Smirnov" etc. So we can't list that. The only explicit test is "bootstrapping permutation test" for the enrichment of TRM core signature overlap. So we will list "bootstrapping permutation test" as the statistical test used in enrichment analysis.

But is "bootstrapping permutation test" explicitly mentioned as "statistical test"? They call it "bootstrapping permutation test" and "statistically significant (P < 0.001) in a bootstrapping permutation test". Yes, that's a statistical test.

Also GSEA uses a "Kolmogorov–Smirnov test" but not explicitly mentioned. So we only list the test that is explicitly mentioned: "bootstrapping permutation test." But also they used GSEA, which itself uses a "permutation test" to compute p-values. They didn't explicitly mention it. So only bootstrapping.

They also mention "hypergeometric test" somewhere? They did not mention it.

Thus for "What statistical test(s) were used in enrichment analysis?" answer: bootstrapping permutation test.

Multiple testing correction: They mention "FDR q-value < 0.25" for GSEA significance threshold. That's a multiple testing correction method. They also mention "FDR" in earlier functional enrichment analysis with GSEA v4.1.1: "The GSEA enrichment plots for the five TRM-related up-regulated and down-regulated gene sets in the TGF-β-treated group. All 10 gene sets shown were significantly enriched at P-value < 0.05 and FDR q-value < 0.25." So yes, multiple testing correction / FDR applied. So answer: Yes.

Custom or specific background gene list? They didn't mention. They mention "We performed GSEA to test whether ...". They didn't mention using a custom background gene list. So "Not described" or "No"? The options: Yes, No or Not described. Since it's not described, answer "Not described".

Now produce a table with six columns:

- Tool
- Version
- Gene set libraries
- Custom background? (Yes/No/Not described)
- Statistical test(s)
- Multiple testing correction?

Wait the question: Provide output in table format. So we need to create a table with six columns: What tool was used, Was enrichment tool version(s) described, Which gene set libraries were used, Does article describe using a custom or specific background gene list? (Yes, No, Not described), What statistical test(s) were used, Was multiple testing correction applied.

But we need to provide a row for each tool? Or combine them? They ask: "Please answer the following 6 questions." Each question corresponds to a column. So we produce one row per question, but we need to include if more than one tool used, list all of them separately. So likely we need a table with 1 row but each column may contain multiple items separated by semicolons or newlines. But they say "If more than one tool, method, or database is used, list all of them separately." But we have only one tool: GSEA. So we can produce a single row.

But maybe they used "GSEA" and "GSEA enrichment plots" is the same tool. They also used "GSEA" for "TRM core signature" overlap? They used a bootstrapping permutation test to compute enrichment p-value. So that is a test. But no other tool. So we can produce a table with one row.

Let's double-check if any other enrichment tool used: They also used "GSEA enrichment plots for the TCM and TEM-related gene sets" in Supplementary S4 Fig. They used GSEA again. So no other tool.

But there is also "Functional enrichment analyses were carried out using GSEA version 4.1.1." That is the only mention of version.

Gene set libraries used: They used GO (Gene Ontology) terms for functional enrichment analysis, and custom tissue-specific TRM gene sets. They also used "Gene Ontology" (GO) for GO terms. Also they used "tissue-specific TRM-associated gene sets" (custom). They didn't mention KEGG, Reactome, etc. So gene set libraries: GO (Gene Ontology). They also used custom gene sets (TRM core signature, tissue-specific TRM gene sets). But those are not standard libraries; they are custom. But we should list all gene set libraries used: GO (Gene Ontology). They also used "tissue-specific TRM-associated gene sets" but those are custom, not a standard library. But they may have used "MSigDB" or "Molecular Signatures Database" for the GSEA sets? They did not mention. So just list GO.

However, they used "GSEA enrichment plots for the five TRM-related up-regulated and down-regulated gene sets." That is a custom gene set library. They also used "Tissue-specific TRM gene sets" custom. But not a standard database. So we list "Gene Ontology (GO)" and "Custom TRM gene sets" (tissue-specific TRM up- and down-regulated gene sets). But the question: Which gene set libraries were used? Identify all gene set libraries or databases the authors queried (e.g., GO, KEGG, Reactome, MSigDB, etc.). Only include what's actually stated in the article. So we can list "Gene Ontology (GO)" and "Custom TRM gene sets" (maybe mention that they used custom gene sets). But we don't know if they used "MSigDB". They didn't mention it. So just GO.

Now, "Does the article describe using a custom or specific background gene list for enrichment analysis? Options: Yes, No or Not described." They didn't mention. So "Not described".

"Which statistical test(s) were used in enrichment analysis?" They mention "bootstrapping permutation test" for enrichment of TRM core signature overlap. They also mention "GSEA" which uses a statistical test internally but not specified. But the question: "State the name(s) of the statistical test(s) used for enrichment analysis (e.g., hypergeometric test, Fisher's exact test). Only include tests linked to enrichment." So the bootstrapping permutation test qualifies. Also, GSEA uses a Kolmogorov-Smirnov-like test, but not explicitly mentioned. So we list "bootstrapping permutation test".

"Was multiple testing correction / FDR applied to enrichment analysis?" They mention "FDR q-value < 0.25" and "P-value threshold alone is not sufficient". They mention FDR q-value. So yes.

Now produce table:

Columns: Tool, Tool version, Gene set libraries, Custom background used? (Yes/No/Not described), Statistical test(s), Multiple testing correction applied?

We need to fill each column.

So for the single row:

Tool: GSEA
Tool version: 4.1.1
Gene set libraries: Gene Ontology (GO); Custom TRM core signature gene sets; Custom tissue-specific TRM gene sets (skin, gut, lung, brain, liver)
Custom background: Not described
Statistical tests: bootstrapping permutation test
Multiple testing correction: Yes

But careful: The custom gene sets: they mention "We found 46–60% of these genes were consistently expressed in a similar manner in our TGF-β-treated groups (Fig 4)." That indicates they used the TRM core signature as custom gene sets. They might have used them as custom gene sets. So we list them as custom gene sets.

The question "Which gene set libraries were used?" includes "GO" which is standard. It also includes "Custom TRM gene sets". But we might consider "custom gene set library" as "gene set library"? The question says "Identify all gene set libraries or databases the authors queried (e.g., GO, KEGG, Reactome, MSigDB, etc.). Only include what's actually stated in the article." So "Custom TRM gene sets" are not a library, but a custom set. But we can still list it if they query them. They did query them. So we can list "Custom TRM core signature gene sets (35 genes)" and "Custom tissue-specific TRM gene sets (up- and down-regulated)". But the question is ambiguous. I'd list "Gene Ontology (GO)" as a library. I'd also mention "Custom TRM core signature" and "Custom tissue-specific TRM gene sets" as custom libraries. But the question says "gene set libraries or databases the authors queried". So yes.

Now produce the table. Let's include each item separately if more than one.

We have only GSEA.

For gene set libraries: GO; Custom TRM core signature; Custom tissue-specific TRM gene sets.

Now produce table:

| Question | Answer |
But they want table format. They ask: "Provide output in table format." So we create a table with columns as questions. Or they want each question as a row? But they want to answer 6 questions. They say "Please answer the following 6 questions." So each row is a question? But the table format should present each question and answer. I think we can create a table with two columns: Question, Answer. And fill each row.

Let's do that.

But they also said "If more than one tool, method, or database is used, list all of them separately." So for each answer, if multiple items, separate by semicolons.

Thus the table:

| # | Question | Answer |
Where # is 1-6.

Let's craft:

1. What tool was used for pathway enrichment analysis? Answer: GSEA

2. Were enrichment tool version(s) described? Answer: GSEA version 4.1.1

3. Which gene set libraries were used? Answer: Gene Ontology (GO); Custom TRM core signature gene sets; Custom tissue-specific TRM gene sets (skin, gut, lung, brain, liver)

4. Does the article describe using a custom or specific background gene list for enrichment analysis? Answer: Not described

5. What statistical test(s) were used in enrichment analysis? Answer: Bootstrapping permutation test

6. Was multiple testing correction / FDR applied to enrichment analysis? Answer: Yes

Now present table.
...done thinking.

| # | Question | Answer |
|---|----------|--------|
| 1 | What tool was used for pathway enrichment analysis? | GSEA |
| 2 | Were enrichment tool version(s) described? | GSEA 4.1.1 |
| 3 | Which gene set libraries were used? | Gene Ontology (GO); Custom TRM core signature gene sets (35 genes); Custom tissue‑specific TRM gene sets (up‑ and down‑regulated sets from skin, gut, lung, brain, and liver) |
| 4 | Does the article describe using a custom or specific background gene list for enrichment analysis? | Not described |
| 5 | What statistical test(s) were used in enrichment analysis? | Bootstrapping permutation test |
| 6 | Was multiple testing correction / FDR applied to enrichment analysis? | Yes |