Run Analysis

1. The gene expression matrix must have "Symbol" as the first column for Gene symbols, followed by columns representing expression levels for each sample (with sample names as column headers).
2. There should be between 2 and 10 sample categories, with at least 10 negative and 10 positive samples. The matrix must contain more than 100 genes.
3. Expression values can be normalized or unnormalized (e.g., Count, TPM, FPKM), and each gene should have a non-zero expression in at least 80% of the samples.
4. The file must be in 'CSV' format.

Example:

Transcriptomic data of islet samples from 58 patients who underwent pancreatic resection (GSE76895), including 30 cases with type 2 diabetes (T2D, positive samples) and 28 non-diabetes cases (ND, negative samples).

1. The first column should be the sample name (with the column name "Sample"), the second column should be the sample category label (with the column name "Class"), and the third column should represent the rank corresponding to the sample category label, with negative to positive samples labeled as integers starting from 0 (column name: "Rank").
2. The "Sample" column in the sample info matrix must match the expression matrix sample names exactly.
3. Additional columns like gender and age can be added.
4. Column names can only consist of letters, numbers, and underscores.
5. Ensure no NA values in the matrix.
6. The file must be in 'CSV' format.

Example:

• Sample: Names of the 58 samples.
• Class: Category corresponding to each sample; T2D represents type 2 diabetes, while ND represents non-diabetes.
• Rank: Label corresponding to the sample category, represented as an integer starting from 0.
• Fasting_glucose: The fasting blood glucose value of the sample; higher values are typically positively correlated with the severity of diabetes.

Specify the category of negative samples used for analysis (the leftmost category).

Specify the category of positive samples used for analysis (the rightmost category).

The threshold used to extract reversal gene pairs. The value must be between 0.3 and 1, with a default of 0.5. A higher threshold results in fewer gene pairs.

Some gene pairs satisfying the threshold may contain the same gene. If you choose to deduplicate, only the gene pair with the highest reversal ratio will be retained. The default is not to deduplicate.

1. Present in a single column, with the column name being the gene set name. The Gene symbol in this column must exist in the "Symbol" column of the expression matrix.
2. The file must be in 'CSV' format.

Example:

Beta identity and maturity: β cells are closely related to type 2 diabetes, so it is important to analyze the perturbation degree of the Beta identity and maturity gene sets.

Specify the sample information to be used in the analysis. It must be assigned along with Sample Category and Data Type.

Specify the sample category to be used in the analysis. It must be assigned along with Sample Information Category and Data Type.

Specify the data type of the sample information. It must be assigned along with Sample Information Category and Sample Category.