2026-10-07T06:28:43Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33475780 2026-09-16T11:45:27Z category_24208 category_24175 category_24193 category_24622 category_24178 item_type_3 month_year_09_2026

Transcriptional memory: prediction and identifiability — analysis release Jorge Mata-Garrido (24666928) Bioinformatics and computational biology not elsewhere classified Systems biology Genomics and transcriptomics Immunogenetics (incl. genetic immunology) Biochemistry and cell biology not elsewhere classified transcriptional memory response transfer history-dependent transcription cellular memory gene expression transcriptomics systems biology computational biology trained immunity mechanistic inference predictive modelling partial identification gene regulatory responses stimulus history CBX3 HP1γ interferon signalling reproducible research <p dir="ltr">Analysis code, retained inputs, derived measurements and numerical outputs accompanying the study</p><p dir="ltr">"Calibrated interventions, not residual expression, identify signaling-independent transcriptional</p><p dir="ltr">memory" (Yu, Desterke & Mata-Garrido).</p><p><br></p><p dir="ltr">The study separates two questions that the transcriptional-memory and trained-immunity literatures</p><p dir="ltr">usually treat as one: whether a primed transcriptional response carries transferable predictive</p><p dir="ltr">information, and whether that information identifies the mechanism maintaining it. It evaluates</p><p dir="ltr">gene-specific response transfer under strict information restrictions in public RNA-seq datasets,</p><p dir="ltr">reserving whole donors, whole challenges and whole ligand pairs from calibration. It then states</p><p dir="ltr">and proves a sharp lower bound on the signaling-independent component of a persistent response,</p><p dir="ltr">and shows that the bound is informative only when the efficacy of the maintenance intervention is</p><p dir="ltr">calibrated on the same scale as the response itself.</p><p><br></p><p dir="ltr">Contents:</p><p dir="ltr">- Analysis code for every reported evaluation</p><p dir="ltr">- Retained input tables and derived measurements</p><p dir="ltr">- Every primary reserved prediction, with its control definitions and uncertainty calculations</p><p dir="ltr">- The frozen local analysis specifications, with SHA-256 hashes and recorded access timestamps</p><p dir="ltr">- Per-panel source mappings (SOURCE_DATA_MAP.csv) linking each manuscript figure to its numerical table</p><p dir="ltr">- Environment information and file checksums</p><p><br></p><p dir="ltr">Unfavourable and domain-incompatible observations are retained rather than filtered. No new</p><p dir="ltr">experimental data were generated.</p><p><br></p><p dir="ltr">Underlying data are public: NCBI Gene Expression Omnibus accessions GSE273837, GSE260996,</p><p dir="ltr">GSE150196, GSE150197, GSE294918, GSE294915, GSE294916 and GSE249136. Published source-data</p><p dir="ltr">workbooks and chromatin summary tables remain attributed to their original studies and are cited</p><p dir="ltr">in the manuscript.</p> 2026-09-16T11:45:27Z Dataset Dataset 10.6084/m9.figshare.33475780.v2 https://figshare.com/articles/dataset/Theoretical_CBX3/33475780 CC BY 4.0