Introduction
GeneSpring GX provides powerful, easy-to-express tools for rapid visualization and analysis of genomic structural variation data. It is the first software that can simultaneously interpret exome microarray, proteomics and metabolomics experiments, and is used for gene expression analysis, genome copy number analysis, genome-wide association analysis, and transcriptomics data analysis. GeneSpring GX provides an interactive desktop computing environment that promotes the understanding of microarray data in the biological range.
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Features:
1. The genome copy number can be analyzed to determine the genome copy number variation area, allele-specific copy number variation and other common mutations, and samples of different groups can be analyzed.
2. Whole genome association analysis.
3. Analyze transcriptome data, detect alternative splicing events, and identify differentially expressed genes and small RNA molecules.
4. Use principal component analysis, clustering methods, and powerful class prediction algorithms to reveal the biological patterns in the provided data.
Some functions of GeneSpring GX use Python's application programming interface (API) and the fully integrated R programming language. For different experimental types, such as gene expression, genome copy number, and genotyping, annotations and data are displayed and overwritten in a new dynamic genome browser. The software also integrates biological function GO analysis, genome enrichment analysis (GSEA), genome analysis (GSA), and statistically significant results in pathway analysis, which facilitates the correlation of data analysis results with biological processes. It is also possible to construct biological networks. GeneSpring can simultaneously analyze multiple types of experimental data, such as small RNA, gene expression, genotyping, and copy number, etc. in one window. This allows users to switch back and forth between data as needed without having to load each experiment individually, making data analysis more concise.
GeneSpring can analyze a variety of expression data, including the following:
Agilent Single Color Expression Data；Agilent TwoColor Expression Data；Affymetrix Expression Data；Illumina Data；GenericSingle Color Expression Da；Generic Two Color Expression Data;Agilent Exon Expression Data;AffymetrixExon Expression Data;Affymetrix Exon Splicing Data。
1 case analysis
GeneSpring GX is powerful and can help beginners quickly complete analysis requirements after mastering the operation process.
Taking the RNA-seq data downloaded in GEO as an example, its processing process is divided into the following 8 steps:
1. Create an experiment and import data
2. Summary report
Shows a summary view of the experiment created. It shows a Box Whisker chart with samples on the X axis and the expressed log value on the Y axis. The sample processing details are shown at the top. If the number of samples exceeds 30, it will be shown in table form.
3. Experimental grouping
Add parameters to help define the grouping of experiments. You can create a parameter by clicking the Add parameter button. First select the desired sample and enter the value to assign the sample value.
4. Sample quality control
The quality control of the software only supports Agilent single-color and dual-color expression data, Affymetrix expression data, Illumina Data, and Affymetrix exon expression data
5. Filter probe
By default, this operation will delete the lowest 20% of all intensity values and generate a profile map of the filtered sample.
6. Significance analysis
According to the experimental grouping, GS 9.0 performs T test or ANOVA.
7、 Fold Change
8. GO function annotation, and search for significant pathways
GeneSpring GX also includes many other useful functions, the specific processing methods can be found in the documentation.
In the process of epigenetics research, it is often necessary to combine multiple omics data, for example, there is a certain relationship between the expression level of genes and the degree of DNA methylation. GeneSpring GX can standardize these data, such as RNA-seq, and can fully study the relationship between these omics data and epigenetic mutations such as DNA methylation or histone modification.
When the editor was preparing the content, I also saw the friendly forces' attention to GeneSpring. There are many specific usage and application examples, as well as public classes about GeneSpring, etc. Interested friends can view the extended reading.
Reading Skills for WeChat Official Account Soft Articles:
Collection of articles and catalogs are not enough? ! Then search for whatever you want! ! !
Extended reading of the GeneSpring series of articles:
Use of genespring-how to make a gene matrix file
Use of genespring-looking for differentially expressed genes
Take you to know a powerful gene expression expert-GeneSpring
GeneSpringGX Chinese Course (2)-GeneSpring GX Terminology and Concepts (1)
GeneSpring GX tutorial (3)-Affymetrix gene chip analysis