Construction of a 5-feature gene model by support vector machine for classifying osteoporosis samples

Figures & data

Table 1. Sample information of datasets

Data set	Expression	Platforms
GSE56116
Normal	3	GPL4133
Osteoporosis	10
GSE62402
High BMD	5	GPL5175
Low BMD	5
GSE35959
Normal	9	GPL570
Osteoporosis	5
GSE13850
High BMD	20	GPL96
Low BMD	20
GSE56814
High BMD	42	GPL5175
Low BMD	31
GSE56815
High BMD	40	GPL96
Low BMD	40
GSE7429
High BMD	10	GPL96
Low BMD	10

Figure 1. Work flow chart

Figure 2. Screening of differentially expressed genes. (a) Volcano plot of differentially expressed genes in dataset GSE56116; (b) Heat map of differentially expressed genes

Figure 3. Functional enrichment of differentially expressed genes. (a) BP annotation of differentially expressed genes; (b) CC annotation of differentially expressed genes; (c) MF annotation of differentially expressed genes; (d) KEGG annotation of differentially expressed genes

Figure 4. PPI analysis of the gene of the functional module

Figure 5. Functional enrichment of functional module genes. (a) BP annotation of functional module genes; (b) CC annotation of functional module genes; (c) MF annotation of functional module genes; (d) KEGG annotation of functional module genes

Figure 6. Identification of Hub genes. (a) PPI network diagram of hub genes obtained by Closeness algorithm. (b) PPI network diagram of hub genes obtained by MCC algorithm. (c) PPI network diagram of hub genes obtained by MNC algorithm. (d) PPI network of hub genes obtained by Degree algorithm

Figure 7. Venn diagram of hub genes identification

Figure 8. Development and verification of the model. (a) The classification result and ROC curve of the GSE35959 dataset sample by the diagnostic model; (b) The classification result and ROC curve of the GSE62402 dataset sample by the diagnostic model. (c) The classification result and ROC curve of the GSE13850 dataset sample by the diagnostic model; (d) The classification result and ROC curve of the GSE56814 dataset sample by the diagnostic model; € The classification result and ROC curve of the GSE56815 dataset sample by the diagnostic model; (f) The classification result and ROC curve of the GSE7429 dataset sample by the diagnostic model

Availability of data and materials

The data that support the findings of this study are openly available in GSE35959 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35959], GSE62402 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi], GSE13850 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi], GSE56814 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi], GSE56815 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi], and GSE7429 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi] datasets.