Tissue-specific Expression Analysis¶
Currently, the tissue-specific patterns analysis provide valuable information about their potential functions for further studies.
Read before use¶
Users need to prepare two files, gene expression matrix and metadata information.
The gene expression matrix: The first column is Geneid, other columns are data. The name of first column must be Geneid. Data from excel (format: xlsx).
The metadata: The first column is sample names, the second column is treatment conditions, and the third column is group names. Colnames must be Samples, Names, and Groups. Data from excel (format: xlsx).
Note: The order of the sample names in both files must be consistent.
tau value calculator¶
This tool provides a tau value calculator. The tau values varies from 0 to 1. Gene with tau value close to 1 represented tissue specificity of gene expression, while gene with tau value close to 0 indicated sharing of gene expression across different tissues.
Input example data: Gene expression matrix, Metadata information.
Venn plot¶
This tool provides vennplot for tissue-specific gene expression. Tissue-specific genes are a class of genes whose functions and expressions are preferred in one or several tissues restrictedly. Identification of tissue-specific genes is essential for discovering multi-cellular biological processes such as tissue-specific molecular regulations, tissue development, physiology, and the pathogenesis of tissue-associated diseases.
Users need to prepare two files, gene expression matrix and metadata information.
The gene expression matrix: The first column is Geneid, other columns are data. The name of first column must be Geneid. Data from excel (format: xlsx).
The metadata: The first column is sample names, the second column is treatment conditions, and the third column is group names. Colnames must be Samples, Names, and Groups. Data from excel (format: xlsx).
Note: The order of the sample names in both files must be consistent.
Input example data: Gene expression matrix, Metadata information.
Bubble Plot¶
This tool provides a bubble plot, which shows gene expression specificity (indicated by dot size and color) among tissues.
Users need to prepare three files, gene expression matrix, metadata information, and genes list.
The gene expression matrix: The first column is Geneid, other columns are data. The name of first column must be Geneid. Data from excel (format: xlsx).
The metadata: The first column is sample names, the second column is treatment conditions, and the third column is group names. Colnames must be Samples, Names, and Groups. Data from excel (format: xlsx).
The gene list: The first column is Geneid. The name of first column must be Geneid. Data from excel (format: xlsx).
Note: The order of the sample names in both gene expression matrix and metadata information files must be consistent.
Input example data: Gene expression matrix, Metadata information, Gene list.
