Microarray expression analysis of genes involved in innate immune memory in peritoneal macrophages.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26981372", "kind": "science-record", "revision": 7, "content_hash": "sha256:a8979509e020f30851351899bbfff09f6e0f7a3948dc0c5a817900f927613ea0", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T21:58:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Microarray expression analysis of genes involved in innate immune memory in peritoneal macrophages.", "doi": "10.1016/j.gdata.2015.11.028", "pmid": "26981372", "authors": ["Keisuke Yoshida", "Claire Renard-Guillet", "Kentaro Inoue", "Katsuhiko Shirahige", "Mariko Okada-Hatakeyama", "Shunsuke Ishii"], "journal": "Genomics data", "year": 2016, "abstract": "Immunological memory has been believed to be a feature of the adaptive immune system for long period, but recent reports suggest that the innate immune system also exhibits memory-like reaction. Although evidence of innate immune memory is accumulating, no in vivo experimental data has clearly implicated a molecular mechanism, or even a cell-type, for this phenomenon. In this study of data deposited into Gene Expression Omnibus (GEO) under GSE71111, we analyzed the expression profile of peritoneal macrophages isolated from mice pre-administrated with toll-like receptor (TLR) ligands, mimicking pathogen infection. In these macrophages, increased expression of a group of innate immunity-related genes was sustained over a long period of time, and these genes overlapped with ATF7-regulated genes. We conclude that ATF7 plays an important role in innate immune memory in macrophages.", "claims": [{"id": "claim-method", "statement": "Briefly, after a log2 transformation of the signal, a linear model was fitted to each sample to assess variability, and comparisons of groups of interest were made using the empirical Bayes test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981372", "locator": "sections[7] \"Statistical analysis of the microarray data sets\" paragraph 2", "quote": "Briefly, after a log2 transformation of the signal, a linear model was fitted to each sample to assess variability, and comparisons of groups of interest were made using the empirical Bayes test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data is available at the GEO database under:\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71111.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981372", "locator": "sections[2] \"Direct link to deposited data[provide URL below]\" paragraphs 1-3", "quote": "The data is available at the GEO database under:\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71111."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using limma with Benjamini–Hochberg correction on GEO dataset GSE71111, the study found that 43.6% of LPS-induced DEGs were regulated by ATF7, supporting the conclusion that ATF7 plays an important role in innate immune memory in macrophages.", "kind": "quantitative", "target": {"value": 43.6, "unit": "per cent", "tolerance": null, "source": "A significant fraction of the LPS-induced DEGs was regulated by ATF7 (43.6%, 51/117, chi-square test, P = 9.9 × 10− 158)."}, "evidence": [{"asset": "source:pmid:26981372", "locator": "sections[9] \"Results\" paragraph 2", "quote": "A significant fraction of the LPS-induced DEGs was regulated by ATF7 (43.6%, 51/117, chi-square test, P = 9.9 × 10− 158)."}, {"asset": "source:pmid:26981372", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We conclude that ATF7 plays an important role in innate immune memory in macrophages."}, {"asset": "source:pmid:26981372", "locator": "sections[7] \"Statistical analysis of the microarray data sets\" paragraph 2", "quote": "Comparison of the expression levels was then performed using the R package ‘limma’ [3]."}, {"asset": "source:pmid:26981372", "locator": "sections[7] \"Statistical analysis of the microarray data sets\" paragraph 2", "quote": "The resulting P values were corrected for multiple comparisons tests according to the Benjamini-Hochberg method [2]."}, {"asset": "source:pmid:26981372", "locator": "sections[2] \"Direct link to deposited data[provide URL below]\" paragraph 2", "quote": "The data is available at the GEO database under:"}, {"asset": "source:pmid:26981372", "locator": "sections[2] \"Direct link to deposited data[provide URL below]\" paragraph 3", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71111."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using limma with Benjamini–Hochberg correction on GEO dataset GSE71111, the study found that 43.6% of LPS-induced DEGs were regulated by ATF7, supporting the conclusion that ATF7 plays an important role in innate immune memory in macrophages.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26981372"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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