I have Sorghum expression data related to drought stress that I obtained from the National Center for Biotechnology Information (NCBI), Expression Omnibus (GEO) database, I need to select the expression pattern of one gene family from this RNA-seq data, I have no idea how to do it, it would be helpful if someone suggested me how to do so. Thank you.
You did not say what kinds of data you have downloaded. There are flat files with normalized data, microarray data, and RNA-seq sequencing data. Microarray and RNA-seq data usually need to be processed with software pipelines to obtain raw data, which must be normalized before they can be used for analysis. Such a process is usually call data preprocessing and is very complicated process.
Hello Wei, The data is RNA-seq. So What would you suggest to me knowing that I'm not familiar with data preprocessing? Thank you in advance.
Hi,
Usually you can also download a processed Count table, which has gene names on Y axis and sample names on X axis and respective expression values in the table itself. If you download raw fastq files, you need certain skills and computational powers to do the raw analysis (like bash programming, using Terminal, running pipelines for demultiplexing, trimming, mapping, counting etc). So if you are not familiar with that I would suggest to try to find the final Count table, which is sometimes provided with the original sequencing files.
To check the expression of a particular gene family, you can simply obtain the respective gene names and search for them in the Count table. Some tables do not have gene names, but contain Ensembl gene ID, which start with ENSG prefix. Then you can make an expression heatmap. To find the genes, related to certain groups, you can utilise databases like "Gene Ontology", "KEGG", "BioCyc", "PANTHER", "Reactome" etc.
Good luck,
Michail
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