RiteeshGrandhi/sciclaimeval-shared-task huggingface dataset:
Conclusion
In conclusion, our findings indicate that the subchondral bone plays important roles in OA progression. Understanding the mechanisms by which subchondral bone is involved in OA development and progression will greatly improve the diagnosis, treatment, and prognosis of OA patients. However, further investigations are necessary to validate the correlation between the key genes identified in this study and immune infiltration and elucidate the roles of these factors in OA progression.
Supplemental Information
(A) Immune cell correlation. (B) The abundance score of immune cells in subchondral bone samples.

Analysis of differential gene expression of all datasets

Analysis of differential gene expression of all datasets

Analysis of differential gene expression of all datasets

Analysis of differential gene expression of all datasets

Analysis of differential gene expression of all datasets

Analysis of differential gene expression of all datasets

Analysis of differential gene expression of all datasets

Analysis of differential gene expression of all datasets
Figure 1: Flow chart depicting the OA gene expression analysis study process.
The DEGs between the lesioned and preserved tibial plateaus of OA patients in the GSE51588 dataset were identified. Functional annotation and PPI network analysis were conducted on the lesioned and preserved sides to explore potential therapeutic targets in OA subchondral bones. Multiple tissues were used to screen for coexpressed genes in OA, and the expression levels of the identified candidate DEGs were measured by qRT–PCR. An immune infiltration analysis was also conducted.

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DOI: 10.7717/peerj.17417/fig-1
Figure 2: Volcano plot and heatmap of DEGs between lesioned and preserved subchondral bone tissues.
(A) Volcano plots displaying the DEG results, where the x- and y-axes represent the log-transformed threshold values. Red dots indicate all significantly upregulated genes, and blue dots indicate all significantly downregulated genes that passed the screening threshold. Yellow dots represent genes that did not demonstrate a significant change. (B) DEGs selected by volcano plot filtering (—logFC— > 1 and P < 0.05).

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DOI: 10.7717/peerj.17417/fig-2
Figure 3: GO and KEGG pathway enrichment analyses of upregulated genes.
GO functional classification of DEGs. The x-axis represents the number of DEGs, with individual GO terms plotted on the y-axis. The graph displays only significantly enriched GO terms (P < 0.05). All GO terms were grouped into three categories: (A) BP analysis, (B) CC analysis, and (C) MF analysis. (D) KEGG pathway analysis. The x-axis represents the number of DEGs annotated in a pathway, with individual KEGG terms shown on the y-axis. The graph displays only significantly enriched KEGG terms (P < 0.05).

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DOI: 10.7717/peerj.17417/fig-3
Figure 4: GO and KEGG pathway enrichment analyses of downregulated genes.
GO functional classification of DEGs. The x-axis represents the number of DEGs, with individual GO terms plotted on the y-axis. The graph displays only significantly enriched GO terms (P < 0.05). All GO terms were grouped into three categories: (A) BP analysis, (B) CC analysis, and (C) MF analysis. (D) KEGG pathway analysis. (D) KEGG pathway analysis. The x-axis represents the number of DEGs annotated in a pathway, with individual KEGG terms shown on the y-axis. The graph displays only significantly enriched KEGG terms (P < 0.05).

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Figure 5: A PPI network map was used to screen for the DEGs in lesioned and preserved subchondral bone tissues.
(A) Network interactions with a score > 0.99, including 116 nodes, were visualized with Cytoscape software. (B) The top 10 hub genes identified by the MCC included JUN, TNF, IL-1β, LEB, CXCL8, and FN1.

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Figure 6: Screening for coexpressed genes in multiple tissues revealed LRRC15 and Col11A1.
The Venn diagram represents the intersections of coexpressed genes across different datasets. The six datasets included cartilage, subchondral bone, and synovial tissue. The species are human and rat. Different colors and numbers represent the number of coexpressed genes across different datasets.

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Figure 7: Validation of coexpressed genes in multiple tissues via qRT–PCR.
Relative expression of LRRC15 and COL11A1 in subchondral bone (A), chondrocyte (B), and fibroblast-like synovial (C) tissue samples, as determined by qRT–PCR. Each column represents the mean ± SD. The OA group exhibited higher expression levels of LRRC15 and COL11A1 than did the normal group. MT represents remedial tibia samples (significant degeneration, lesioned), and LT represents lateral tibia samples (minimal degeneration, preserved). IL-1β (10 ng/ml) was added to SF and chondrocytes for 48 h for further analysis. *P < 0.05 vs. the normal group; **P < 0.01 vs. the normal group; ***P < 0.001 vs. the normal group; ****P < 0.0001 vs. the normal group; n = 3. The experiment was repeated at least three times.

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Figure 8: Differences in immune infiltration between lesioned and preserved subchondral bone tissues.
(A–H) Differences in immune infiltration between lesioned and preserved subchondral bone tissues. MT represents remedial tibia samples (significant degeneration, lesioned), which are marked in green. LT represents lateral tibia samples (with minimal degeneration, preserved), which are marked in brown. P values < 0.05 were considered to indicate significance.

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DOI: 10.7717/peerj.17417/fig-8
Screening coexpressed DEGs using multiple datasets.
Gene primers.