Shulou(Shulou.com)06/01 Report--

Today, I will talk to you about what the pseudotime in the single-cell transcriptional group is. Many people may not know much about it. In order to make you understand better, the editor has summarized the following contents for you. I hope you can get something according to this article.

For single cell transcriptome data, we can get cell subtypes through cluster analysis, and then through difference analysis, we can get different cell subtypes of marker genes. Combined with downstream functional analysis, we can have a better understanding of cell types and functions.

These are the basic analysis contents of the single cell transcriptome. For the identified cell subtypes, we can further study the process of differentiation and evolution between different subtypes. In an organism, cell differentiation is a dynamic process, which is affected by many factors, such as cell-cell interaction, biomolecule regulation and so on, and the process of each cell differentiation is not synchronized. If cell differentiation is regarded as a process of climbing stairs, the floor of each cell is different at the same time.

Regarding the process of cell differentiation as a timeline, the study determines the position of each cell on the timeline, which is the so-called pseudotime analysis, also known as simultaneity analysis, or cell trajectory cell trajectory analysis.

Through sequencing, we obtained the expression data of genes in different cells, and then carried out timing analysis based on the expression data, which usually included the following three steps.

1. Screening gene

The selection of genes is very important for follow-up analysis, and different gene assemblies get completely different results. From the quantitative results, we can see that the expression of many genes is very low, some of which is background noise, which needs to be removed in the follow-up analysis. in addition, in order to improve the accuracy of the analysis results, we need to select biologically meaningful genes, such as marker gene for follow-up analysis.

two。 Dimension reduction

Gene expression is a high-dimensional data structure, direct analysis based on such data is very complex and tedious, the amount of computation is very large, so we need to reduce the dimension first.

3. Pseudotime

The process of cell differentiation is similar to that of species evolution, which is a tree structure. First, an optimal tree structure is constructed according to the distribution of expression, and then the position of each cell in the tree structure is determined.

The results of a typical timing analysis are as follows

A 2D-plot is used to show the cell trajectory, so it is necessary to reduce the dimension in the dividing process, each point in the picture represents a cell, and the dendritic structure behind the cell is the dendritic structure of cell differentiation.

After obtaining the pseudotime of the cell, we can analyze the difference according to pseudotime and explore the important genes in the process of cell differentiation, as shown below.

Finally, functional enrichment analysis and gene interaction analysis can be combined to mine important functional genes.

After reading the above, do you have any further understanding of what pseudotime is in the single-cell transcriptome? If you want to know more knowledge or related content, please follow the industry information channel, thank you for your support.

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