Fig. 5

De novo assembled novel transcripts in mouse preimplantation embryos. a Length distribution for de novo assembled novel transcripts. Candidate novel transcripts with lengths less than 500 bp were filtered out. b Exon number distribution for de novo assembled novel transcripts. Candidate novel transcripts with lengths less than 500 bp were filtered out. c Intron length distribution for novel candidate transcripts. The introns of novel candidate genes were slightly longer than annotated introns, on average. d Hierarchical clustering analysis of novel transcripts, which shows stage-specific expression of genes in mouse preimplantation embryo samples. These genes can be divided into three major clusters: cluster I are early zygotic genes which are expressed during the zygote stage and then are down-regulated at later stages; cluster II are maternal genes, which account for over 60 % of novel genes; cluster III are late zygotic genes which start to be expressed from the two-cell stage. e The total FPKM of all 913 novel genes in each embryonic stage, showing enrichment in the embryo stages before the eight-cell stage, especially in zygotes. f Principal component (PC) analysis of mouse preimplantation embryos based on the 913 novel transcripts