Learning DAVID Database (1)

Introduction:

DAIVD is a bioinformatics database and free online analysis software that helps users extract systematically comprehensive biological function annotation information (term) from large-scale gene or protein lists.Mainly used for differential gene function and pathway enrichment analysis.Web page: DAVID: Functional Annotation Result Summary

Official exercise data for users without gene numbers demolist1 and demolist2

https://david.ncifcrf.gov/helps/demo1.txthttps://david.ncifcrf.gov/helps/demo2.txt

demolist1 recorded up-regulation of 164 differentially expressed genes found in CD4+/CD62L-T cells relative to CD4+/CD62L-T cells

The content of the uploaded txt file can be gene ID or gene name. Different gene names are separated by newlines.

DAVID Gene ID Conversion Tool

Common genetic databases are Ensembl or NCBI

Enter gene ID: 3781 in the open NCBI web search box to find related gene information:

KCNN2 is the gene name and 3781 is the gene ID of KCNN2, both of which can be used as input data for DAVID

Upload bar action:

Copy the gene name or gene ID in the txt file to box A, or directly to the txt file

select identifier selection bar

entrez_gene_id: Gene ID corresponding to the number of uploaded dataofficial_gene_symbol : The corresponding uploaded data is the gene name

step3 Click Gene List

step4 Click Submit List , the page content is updated to step2:

After submitting the gene list, step 2 uses multiple analysis directions, ①Functional Annotation Tool function for gene enrichment analysis, ②Gene ID Conversion Tool function for gene ID conversion, for example, convert the ID number of the NCBI gene library to the gene number of the Ensembl library (both correspond to the same gene)

Find species Latin name:

When performing gene ID conversion, you need to specify the species to be converted, and you need to enter the Latin name of the substance or the corresponding species ID number, such as human Latin homo sapiens, corresponding species ID: 9606

You can find the Latin name and corresponding species ID of the required species in the NCBI webpage

①Select the search range Taxomomy (taxonomy) from the drop-down box -->②Enter the English name of the target species, such as mouse mouse --> Click search -->③Show the matched species information

Gene ID conversion:

①There are 2500 gene IDs uploaded in the video, and 2355 human genes and 1 unknown gene are matched in the database

②Select the ID format you want to convert from the drop-down box, and select official_gene_symbol in the video, which is the official gene name

③Specify the species to which the gene belongs

④Click submit to convert and wait for the conversion to complete

①5 The status of conversion, successful indicates that the conversion is successful

②From column, is the uploaded genetic data

③To column, is the result of conversion, according to the selected official_gene_symbol, the converted gene name

④To column is just the abbreviation of gene name, David Gene Name column is the complete gene name

Click the Download File above to download the txt file and open it with Excel

Reference video link:

Introduction to gene enrichment tool DAVID (1)-Gene ID conversion_bilibili