Table 1..
A cartilage histopathology grade assessment-dgrading methodology.
Fig 1.
HE staining results of cartilage tissue in different groups of rat PTOA (A: normal group, B: mild PTOA group, C: severe PTOA group).
Fig 2.
Safranin O fast green staining results of cartilage tissue in different groups of rat PTOA (A: normal group, B: mild PTOA group, C: severe PTOA group).
Fig 3.
The proportion of identified metabolites in various chemical classifications.
Fig 4.
a. Positive ion mode volcanic map (color and up-regulation correlation with differential metabolites) (A) Mild PTOA Group VS Severe PTOA Group (B) Mild PTOA Group VS Normal Group (C) Severe PTOA Group VS Normal Group. b. Negative ion mode volcanic map (correlation between color and up-regulation of differential metabolites) (A) Mild PTOA Group VS Severe PTOA Group (B) Mild PTOA Group VS Normal Group (C) Severe PTOA Group VS Normal Group.
The x-axis in the graph shows the logarithmic value of log2 for the fold change, while the y-axis represents the logarithmic value of -log10 for the significance p value. Metabolites that show significant differences are shown in rose red if they meet the criteria of FC >1.5 and p value <0.05. Metabolites that meet the criteria of FC < 0.67 and p value < 0.05 are shown in blue. Metabolites that are not significantly different are shown in black. The marked metabolites in the graph are the ones that show significant differences, and they are labeled with their qualitative names. The top 10 upregulated and top 10 downregulated metabolites are indicated with their respective fold change values (FC).
Fig 5.
a. Positive ion multi-dimensional analysis chart (A) Mild PTOA group VS Severe PTOA group (B) Mild PTOA group VS normal group (C) Severe PTOA group VS Normal group (a) 3D PCA score chart (b) PLS-DA score chart (c) PLS-DA replacement test (d) OPLS-DA score chart (e) OPLS-DA replacement test. b. Multidimensional analysis of negative ions (A) Mild PTOA group VS Severe PTOA group (B) Mild PTOA group VS normal group (C) Severe PTOA group VS normal group (a) 3D PCA score chart (b) PLS-DA score chart (c) PLS-DA replacement test (d) OPLS-DA score chart (e) OPLS-DA replacement test.
Table 2.
Negative ion mode significant differential metabolites (Fold Change greater than 2 or less than 0.5).
Table 3.
Positive ion mode significant differential metabolites (Fold Change greater than 2 or less than 0.5).
Fig 6.
a. Positive ion mode significant difference metabolite expression difference factor analysis (A) mild PTOA group VS severe PTOA group (B) mild PTOA group VS normal group (C) Severe PTOA group VS normal group. b. Negative ion mode significant difference metabolite expression difference factor analysis (A) mild PTOA group VS severe PTOA group (B) mild PTOA group VS normal group (C) Severe PTOA group VS normal group.
The abscissa in the figure indicates the difference expression multiple, red indicates that the difference expression multiple is greater than 1, and green indicates that the difference expression multiple is less than 1. Ordinates indicate significantly differential metabolites.
Fig 7.
a. Positive ion mode, significant difference, metabolite level clustering heat map (A), mild PTOA group VS severe PTOA group, (B) mild PTOA group VS normal group, (C) severe PTOA group VS normal group. b. Negative ion pattern significant difference metabolite level clustering heat map (A) Mild PTOA group VS severe PTOA group (B) Mild PTOA group VS normal group (C) Severe PTOA group VS normal group.
The figure illustrates differential metabolites, with each row representing a specific metabolite showing significant differential expression. The vertical axis depicts the metabolite, while the horizontal axis represents different sample groups. The color red indicates significant upregulation, while blue signifies significant downregulation, with varying shades reflecting the degree of upregulation or downregulation. Similar expression patterns of metabolites are clustered together on the left side of the figure.
Fig 8.
a Positive ion mode correlation heat map (A) Mild PTOA group VS Severe PTOA group (B) Mild PTOA group VS normal group (C) Severe PTOA group VS normal group. b. Negative ion mode correlation heat map (A) Mild PTOA group VS Severe PTOA group (B) Mild PTOA group VS normal group (C) Severe PTOA group VS normal group.
In this visualization, the color scheme helps us understand the relationship between variables. Red signifies a positive correlation, blue indicates a negative correlation, and white indicates no significant correlation. The intensity of the color reflects the strength of the correlation coefficient - darker colors represent higher degrees of positive or negative correlation. Additionally, the size of the data points conveys the significance of the correlation. A smaller p-value, indicating higher significance, is represented by smaller data points, whereas a larger point size represents lower significance.
Fig 9.
KEGG enrichment pathway chart (bubble chart) (A) mild PTOA group VS severe PTOA group (B) mild PTOA group VS normal group (C) Severe PTOA group VS normal group.
In a bubble chart, each bubble represents a metabolic pathway. The selection criteria for these pathways is based on their p-values, with only the top 20 pathways with the highest significance being included. The horizontal placement and size of each bubble in the chart represent the influence of the pathway in topology analysis. The larger the bubble, the greater the influence of the pathway. The vertical placement and color of each bubble represent the p-value of enrichment analysis. The p-values are converted to their negative logarithm (-log10 p-value) and the darker the color, the smaller the p-value. A smaller p-value indicates a higher degree of enrichment and therefore greater significance in the analysis. Furthermore, the rich factor of each pathway represents the proportion of differential metabolites within the pathway, compared to the total number of metabolites annotated in the pathway.
Fig 10.
Differential abundance scores of differential metabolic pathways (classified according to Pathway_Hierarchy) (A) mild PTOA group VS severe PTOA group (B) mild PTOA group VS normal group (C) severe PTOA group VS normal group.
The figure's Y-axis represents the name of the differential pathway, while the X-axis represents the DA score. The DA score reflects the overall change in all metabolites within the metabolic pathway. A score of 1 indicates an increase in the expression of all identified metabolites in the pathway, while a score of −1 indicates a decrease in their expression. The length of the line segment represents the absolute value of the DA score, and the size of the dot at the end of the line segment indicates the number of metabolites in the pathway. A larger dot signifies a higher number of metabolites. The color intensity of the line segments and dots corresponds to the value of the DA score. The darker red indicates a higher likelihood of overall upregulation in the pathway's expression, whereas the darker blue denotes a higher likelihood of overall downregulation.