Gene expression profiling of Gram-negative bacteria-induced inflammation in human whole blood: The role of complement and CD14-mediated innate immune response.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484252", "kind": "science-record", "revision": 8, "content_hash": "sha256:39480bbc60b4c36137b32ecc67bead004687e560e966f1aa176e122a06e631c5", "created_at": "2026-11-01T15:40:13Z", "updated_at": "2026-11-01T22:42:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiling of Gram-negative bacteria-induced inflammation in human whole blood: The role of complement and CD14-mediated innate immune response.", "doi": "10.1016/j.gdata.2015.05.019", "pmid": "26484252", "authors": ["Corinna Lau", "Ole Kristoffer Olstad", "Marit Holden", "Ståle Nygård", "Hilde Fure", "Knut Tore Lappegård", "Ole-Lars Brekke", "Terje Espevik", "Eivind Hovig", "Tom Eirik Mollnes"], "journal": "Genomics data", "year": 2015, "abstract": "Non-sterile pathogen-induced sepsis and sterile inflammation like in trauma or ischemia-reperfusion injury may both coincide with the life threatening systemic inflammatory response syndrome and multi-organ failure. Consequently, there is an urgent need for specific biomarkers in order to distinguish sepsis from sterile conditions. The overall aim of this study was to uncover putative sepsis biomarkers and biomarker pathways, as well as to test the efficacy of combined inhibition of innate immunity key players complement and Toll-like receptor co-receptor CD14 as a possible therapeutic regimen for sepsis. We performed whole blood gene expression analyses using microarray in order to profile Gram-negative bacteria-induced inflammatory responses in an ex vivo human whole blood model. The experiments were performed in the presence or absence of inhibitors of complement proteins (C3 and CD88 (C5a receptor 1)) and CD14, alone or in combination. In addition, we used blood from a C5-deficient donor. Anti-coagulated whole blood was challenged with heat-inactivated Escherichia coli for 2 h, total RNA was isolated and microarray analyses were performed on the Affymetrix GeneChip Gene 1.0 ST Array platform. The initial experiments were performed in duplicates using blood from two healthy donors. C5-deficiency is very rare, and only one donor could be recruited. In order to increase statistical power, a technical replicate of the C5-deficient samples was run. Subsequently, log2-transformed intensities were processed by robust multichip analysis and filtered using a threshold of four. In total, 73 microarray chips were run and analyzed. The normalized and filtered raw data have been deposited in NCBI's Gene Expression Omnibus (GEO) and are accessible with GEO Series accession number GSE55537. Linear models for microarray data were applied to estimate fold changes between data sets and the respective multiple testing adjusted p-values (FDR q-values). The interpretation of the data has been published by Lau et al. in an open access article entitled \"CD14 and Complement Crosstalk and Largely Mediate the Transcriptional Response to Escherichia coli in Human Whole Blood as revealed by DNA Microarray\" (Lau et al., 2015).", "claims": [{"id": "claim-method", "statement": "For interpretation of the results, which have been published elsewhere [1], the normalized and filtered log2 intensities of the 19,695 passed transcripts and for all 73 arrays were subjected to downstream statistical analyses using linear models for microarray data (Limma Bioconductor) [4], [5]. To correct for multiple testing, FDR q-values were computed from the p-values using the Benjamini–Hochberg method for controlling the false discovery rate (FDR) [6].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484252", "locator": "sections[8] \"Downstream statistical analyses\" paragraph 2", "quote": "For interpretation of the results, which have been published elsewhere [1], the normalized and filtered log2 intensities of the 19,695 passed transcripts and for all 73 arrays were subjected to downstream statistical analyses using linear models for microarray data (Limma Bioconductor) [4], [5]. To correct for multiple testing, FDR q-values were computed from the p-values using the Benjamini–Hochberg method for controlling the false discovery rate (FDR) [6]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The normalized and filtered log2-transformed intensities are available here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55537.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484252", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "The normalized and filtered log2-transformed intensities are available here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55537."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used linear models for microarray data to estimate fold changes and false-discovery-rate-adjusted p-values, and the source data are accessible through NCBI GEO accession GSE55537.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484252", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Linear models for microarray data were applied to estimate fold changes between data sets and the respective multiple testing adjusted p-values (FDR q-values)."}, {"asset": "source:pmid:26484252", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The normalized and filtered raw data have been deposited in NCBI's Gene Expression Omnibus (GEO) and are accessible with GEO Series accession number GSE55537."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used linear models for microarray data to estimate fold changes and false-discovery-rate-adjusted p-values, and the source data are accessible through NCBI GEO accession GSE55537.", "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:26484252"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE55537"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {"fdr_threshold": "with Benjamini–Hochberg false discovery rate correction"}, "inputs": ["data:geo:GSE55537"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484252", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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"uri": null, "sha256": "sha256:bd342ab7ee40213a4f5fa5aae052e9c66a6a9e2931f8e919b58b30bac1e8efdf", "bytes": 10499, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#t0005", "version": null, "note": "List of microarray data sets generated by this study.", "structure": {"pmcid": "PMC4583639", "section_index": 6, "section_title": "DNA microarray analysis", "row_count": 74, "column_count": 5}, "table": {"label": "Table 1", "caption": "List of microarray data sets generated by this study.", "rows": [["GEO sample ID", "Sample title", "CEL file", "Protocol", "Scan date"], ["GSM1338877", "C5DR_anti-CD14 + Compstatin_D1", "10_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day1, replicate 1", "6/5/2010"], ["GSM1338878", "C5DR_anti-CD14 + Compstatin_D1_No2", "10_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338879", "C5DR_anti-CD14 + Compstatin_D2", "10_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338859", "C5D_C5aR antagonist_D1", "11_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338860", "C5D_C5aR antagonist_D1_No2", "11_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338861", "C5D_C5aR antagonist_D2", "11_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, C5aR-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338880", "C5DR_C5aR antagonist_D1", "12_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338881", "C5DR_C5aR antagonist_D1_No2", "12_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338882", "C5DR_C5aR antagonist_D2", "12_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, C5aR-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338862", "C5D_inhibitor ctrl_D1", "13_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338883", "C5DR_inhibitor ctrl_D1", "14_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338863", "C5D_inhibitor ctrl_D1_No2", "15_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338864", "C5D_inhibitor ctrl_D2", "15_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, inhibitor controls, 120 min, day 2", "5/13/2010"], ["GSM1338884", "C5DR_inhibitor ctrl_D1_No2", "16_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338885", "C5DR_inhibitor ctrl_D2", "16_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, inhibitor controls, 120 min, day 2", "5/13/2010"], ["GSM1338816", "ctrl2_PBS_D1", "17_C2_D1.CEL", "Healthy donor 2, PBS, 120 min, day 1", "5/20/2010"], ["GSM1338817", "ctrl2_PBS_D2", "17_C2_D2.CEL", "Healthy donor 2, PBS, 120 min, day 2", "5/28/2010"], ["GSM1338818", "ctrl_PBS_D1", "17_C5_D1.CEL", "Healthy donor 1, PBS, 120 min, day 1", "5/20/2010"], ["GSM1338819", "ctrl_PBS_D2", "17_C5_D2.CEL", "Healthy donor 1, PBS, 120 min, day 2", "5/28/2010"], ["GSM1338820", "ctrl2_E.coli_D1", "18_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, uninhibited, 120 min, day 1", "5/20/2010"], ["GSM1338821", "ctrl2_E.coli_D2", "18_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, uninhibited, 120 min, day 2", "5/28/2010"], ["GSM1338822", "ctrl_E.coli_D1", "18_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, uninhibited, 120 min, day 1", "5/20/2010"], ["GSM1338823", "ctrl_E.coli_D2", "18_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, uninhibited, 120 min, day 2", "5/28/2010"], ["GSM1338824", "ctrl2_Compstatin_D1", "19_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338825", "ctrl2_Compstatin_D2", "19_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, C3-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338826", "ctrl_Compstatin_D1", "19_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338827", "ctrl_Compstatin_D2", "19_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, C3-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338844", "C5D_PBS_D1", "1_C5_D1.CEL", "C5 deficient, PBS, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338845", "C5D_PBS_D1_No2", "1_C5_D1_Nr2.CEL", "C5 deficient, PBS, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338846", "C5D_PBS_D2", "1_C5_D2.CEL", "C5 deficient, PBS, 120 min, day 2", "5/13/2010"], ["GSM1338828", "ctrl2_anti-CD14_D1", "20_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338829", "ctrl2_anti-CD14_D2", "20_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, CD14-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338830", "ctrl_anti-CD14_D1", "20_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338831", "ctrl_anti-CD14_D2", "20_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, CD14-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338832", "ctrl2_anti-CD14 + Compstatin_D1", "21_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338833", "ctrl2_anti-CD14 + Compstatin_D2", "21_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338834", "ctrl_anti-CD14 + Compstatin_D1", "21_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338835", "ctrl_anti-CD14 + Compstatin_D2", "21_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338836", "ctrl2_C5aR antagonist_D1", "22_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338837", "ctrl2_C5aR antagonist_D2", "22_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, C5aR-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338838", "ctrl_C5aR antagonist_D1", "22_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, C5aR-inhibition, 120 min, day 1", "5/20/2010"], ["GSM1338839", "ctrl_C5aR antagonist_D2", "22_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, C5aR-inhibition, 120 min, day 2", "5/28/2010"], ["GSM1338840", "ctrl2_inhibitor ctrl_D1", "24_C2_D1.CEL", "Healthy donor 2, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1", "5/20/2010"], ["GSM1338841", "ctrl2_inhibitor ctrl_D2", "24_C2_D2.CEL", "Healthy donor 2, 5 × E06/mL E.coli, inhibitor controls, 120 min, day 2", "5/28/2010"], ["GSM1338842", "ctrl_inhibitor ctrl_D1", "24_C5_D1.CEL", "Healthy donor 1, 1 × E06/mL E.coli, inhibitor controls, 120 min, day 1", "5/20/2010"], ["GSM1338843", "ctrl_inhibitor ctrl_D2", "24_C5_D2.CEL", "Healthy donor 1, 5 × E06/mL E.coli, inhibitor controls, 120 min, day 2", "5/28/2010"], ["GSM1338865", "C5DR_PBS_D1", "2_C5_D1.CEL", "C5 deficient, C5-reconstituted, PBS, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338866", "C5DR_PBS_D1_No2", "2_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, PBS, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338867", "C5DR_PBS_D2", "2_C5_D2.CEL", "C5 deficient, C5-reconstituted, PBS, 120 min, day 2", "5/13/2010"], ["GSM1338847", "C5D_E.coli_D1", "3_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, uninhibited, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338848", "C5D_E.coli_D1_No2", "3_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, uninhibited, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338849", "C5D_E.coli_D2", "3_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, uninhibited, 120 min, day 2", "5/13/2010"], ["GSM1338868", "C5DR_E.coli_D1", "4_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, uninhibited, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338869", "C5DR_E.coli_D1_No2", "4_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, uninhibited, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338870", "C5DR_E.coli_D2", "4_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, uninhibited, 120 min, day 2", "5/13/2010"], ["GSM1338850", "C5D_Compstatin_D1", "5_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338851", "C5D_Compstatin_D1_No2", "5_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338852", "C5D_Compstatin_D2", "5_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, C3-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338871", "C5DR_Compstatin_D1", "6_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1, replicate 1", "6/3/2010"], ["GSM1338872", "C5DR_Compstatin_D1_No2", "6_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, C3-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338873", "C5DR_Compstatin_D2", "6_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, C3-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338853", "C5D_anti-CD14_D1", "7_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338854", "C5D_anti-CD14_D1_No2", "7_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338855", "C5D_anti-CD14_D2", "7_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, CD14-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338874", "C5DR_anti-CD14_D1", "8_C5_D1.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338875", "C5DR_anti-CD14_D1_No2", "8_C5_D1_Nr2.CEL", "C5 deficient, C5-reconstituted, 1 × E06/mL E.coli, CD14-inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338876", "C5DR_anti-CD14_D2", "8_C5_D2.CEL", "C5 deficient, C5-reconstituted, 5 × E06/mL E.coli, CD14-inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338856", "C5D_anti-CD14 + Compstatin_D1", "9_C5_D1.CEL", "C5 deficient, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 1, replicate 1", "6/5/2010"], ["GSM1338857", "C5D_anti-CD14 + Compstatin_D1_No2", "9_C5_D1_Nr2.CEL", "C5 deficient, 1 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 1, replicate 2", "6/3/2010"], ["GSM1338858", "C5D_anti-CD14 + Compstatin_D2", "9_C5_D2.CEL", "C5 deficient, 5 × E06/mL E.coli, combined C3 and CD14 inhibition, 120 min, day 2", "5/13/2010"], ["GSM1338886", "ctrl2_T0_D2", "K2_T0_Dag2.CEL", "Healthy donor 2, PBS, 0 min, day 2", "5/28/2010"], ["GSM1338887", "ctrl_T0_D2", "K5_T0_Dag2.CEL", "Healthy donor 1, PBS, 0 min, day 2", "5/28/2010"], ["GSM1338888", "C5D_T0_D2", "T0_Dag1_C5_D2.CEL", "C5 deficient, PBS, 0 min, day 2", "5/13/2010"]], "row_count": 74, "column_count": 5, "numeric_cells": 309, "header_rows": 1, "locator": "section[6]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE55537 not downloaded", "asset:data:geo:GSE55537 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fdr_threshold": "with Benjamini–Hochberg false discovery rate correction"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For interpretation of the results, which have been published elsewhere [1], the normalized and filtered log2 intensities of the 19,695 passed transcripts and for all 73 arrays were subjected to downstream statistical analyses using linear models for microarray data (Limma Bioconductor) [4], [5]. To correct for multiple testing, FDR q-values were computed from the p-values using the Benjamini–Hochberg method for controlling the false discovery rate (FDR) [6]."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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