2026-10-14T12:02:49Z
https://api.figshare.com/v2/oai
oai:figshare.com:article/34035430
2026-09-30T17:33:55Z
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month_year_09_2026
<p>Spatial cohort (GSE248454).</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) Placement of the profiled regions across the tissue microarray, coloured by compartment and shaped by pain group. Histology images were not deposited with the dataset, so this panel shows region placement, not tissue architecture; the marker channels (CD68, CD45, αSMA) guided placement rather than sorting cells. (B) Deconvolution-estimated cellular composition of each region (SpatialDecon with the safeTME reference), which is a coarse compositional control rather than a cell-type assignment. (C) Association with pain by compartment for both discovery-derived hypotheses (Hallmark-EMT and the 35-gene pain-UP signature) in both detection universes. Grey points are the unadjusted permutation results and red points the same tests after Freedman–Lane adjustment for age and log<sub>2</sub> nuclei count, with the arrow showing the shift; purple triangles are the corresponding CAMERA results, which were computed for the Hallmark family only. The dashed line marks the nominal p = 0.05 and is a reading aid, not the inferential threshold: inference rests on the Holm-adjusted values over the family of six, and the only two tests that survive them are labelled. Full numerical results, including Monte-Carlo intervals and the exploratory two-sided family-corrected q-values, are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0346948#pone.0346948.t002" target="_blank">Table 2</a>.</p>
2026-09-30T17:33:45Z
Image
Figure
10.1371/journal.pone.0346948.g002
https://figshare.com/articles/figure/_p_Spatial_cohort_GSE248454_p_/34035430
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