Processing preanalyzed Bulk RNA sequencing data

Question

[nils.simon.biology]

Hi, We sent mouse samples to Novogene to perform bulk RNA sequencing. The samples were mouse tissues from a disease model in which one of the groups was naive and one got the disease. As our group lacks biostatistic and bioninformatic knowledge we also paid them to analyze the data for us. According to their report the mapped the reads to a mouse reference genome and performed Differential Gene Expression Analysis using DESeq2. Now I am sitting in front of an excel file that contains: log2FoldChange; pvalue; padj; gene_name etc. What would be the next steps considering the filtering of the data and the later visualization? Your help would be greatly appreciated!

[lieven.sterck]

usually one proceeds with doing filtering on LogFoldChange (eg < or > 1 ) and/or on padj and/or FDR .

then you will get a list of the 'top' (or highly significant) DEG genes

[nils.simon.biology]

Hi, So I sorted my data with the following criteria: padj value < 0.1

I end up with only 137 genes of which only 123 are protein coding genes.

Is this enough data to perform some kind of visualization analysis (networks e.g.)? If yes is there any free software that could do this?

Or should I do a different filtering approach ?