2026-10-14T08:57:02Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34035433 2026-09-30T17:33:56Z category_12 category_13 category_21 category_734 category_61 category_64 category_132 portal_5 item_type_1 month_year_09_2026

<p>Specificity and context.</p> Diovanni de Paula Ferreira (25145323) Rafael de Negreiros Botan (25145326) Wagner R. Martins (25145329) Iruena M. Kessler (25145332) Cell Biology Genetics Biotechnology Biological Sciences not elsewhere classified Developmental Biology Cancer Infectious Diseases philpott et al aware competitive testing 50 ), related 0022 ), although gene sets matched freedman &# 8211 epithelial &# 8211 ci &# 8722 survive exact phenotype set surviving correction remodeling transcriptional programme transcriptome spatial cohort spatial analysis applied vs 16 less quantification detection filter oa ), yet matrix remodeling rather like synovial stromal compartments ), persisting 50 significantly enriched 36 oa ), 1 ]; gse248454 specific discovery signature remodeling programme associated associated gene program imprecise (+ 0 xlink "> pain level knee pain knee osteoarthritis pain exploratory transcriptomic discovery spatial cohort gene signature xlink "> like stromal knee osteoarthritis &# 8805 level whole hallmark set exploratory program analysis plan 32 knee positively associated pain severity exploratory pain worse patient undirected scan typical region three limits tested specificity <p>(A) Competitive enrichment of the 35-gene pain-UP module in OA versus healthy synovium (GSE89408): the module ranks significantly low relative to the rest of the transcriptome (NES = −1.65, p_adj = 0.039). Panel B shows that this is a relative-ranking result and not a coherent reduction of the programme. (B) Per-gene heatmap of the programme in OA versus healthy synovium, with the per-gene OA-minus-healthy difference alongside, showing whether the reduction is driven by particular genes or is distributed across the set: 16 of 30 genes are lower and 14 higher in OA, median difference −0.04 log₂ units, with four genes significant at FDR < 0.05 in both directions. (C) In OA synovium (GSE283079), the module score is inversely correlated with canonical inflammatory activation.</p> 2026-09-30T17:33:45Z Image Figure 10.1371/journal.pone.0346948.g003 https://figshare.com/articles/figure/_p_Specificity_and_context_p_/34035433 CC BY 4.0