Selecting the genes to verify (statistical significance and biological relevance) the transcripts obtained from RNA-Seq or microarray experiment is totally based on the your biological questions.
Of course, you also select some transcripts whose expression are quietly significant according to sequencing experiment. However, sorting the differentially expressed transcripts (DETs) based on the p-value (even corrected p-value) is not good option always for biological relevance, but it should be good for validating RNA-Seq results.
After comprehensive annotation and evaluation (GO, KEGG, InterPro, Pfam, Ka/Ks ration, transcript expansion or depletion, DET analysis, etc...) of the sequencing data, you should reach a conclusion about the topic you have been discussing, then decide the transcript for qPCR experiment. As you mention the qPCR, of course, the selected transcript you did should exhibit a differences (big or little) in its expression.