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Table 1 Positional classification of the transcriptome of Macrostomum lignano and details on the candidate transcripts selected for validation

From: Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits

Class n % Mean B-A Mean C-B Mean D-C Candidates B-A C-B D-C ISH RNAi
[0,0,0] 70064 93.7 −0.14 −0.09 0.09 RNA815_92.1 1.15 0.55 0.24 X -
Non-diff.       RNA815_40.1 0.82 0.27 0.51 X -
expressed       RNA815_2403.2 −1.08 −0.23 −0.32 X X
       RNA815_2224.1 0.52 −0.02 0.24 - -
[+,0,0] 3360 4.4 4.00 −0.18 −0.41 RNA815_7008 5.17 −0.03 −0.39 X X
Testis region       RNA815_9973.1 5.02 −0.03 −0.41 X X
       RNA815_6628.2 4.13 −0.27 −0.46 X -
       RNA815_3228 4.50 −0.25 −0.67 X -
       RNA815_10311.2 2.89 0.61 −0.14 X -
       RNA815_9262 2.55 0.12 −0.24 X -
[+,+,0] 127 <0.1 3.18 4.14 0.52 RNA815_16738 2.77 4.75 0.77 X -
Ovary region       RNA815_1618.1 5.46 4.35 0.47 X -
       RNA815_2640 3.62 4.40 0.67 X X
       RNA815_7725.2 2.91 4.15 −0.01 X -
       RNA815_7498 2.28 4.92 0.61 X -
       RNA815_12337.1 2.32 6.04 −0.14 - -
[0,+,0] 323 0.4 0.57 3.41 0.36 RNA815_4558 0.39 4.09 0.64 X -
Ovary region       RNA815_6266 2.00 5.35 0.88 - -
[0,0,+] 366 0.4 −0.02 −0.03 4.23 RNA815_22046 0 1.00 7.69 X -
Tail region       RNA815_80.4 0 0 8.30 X X
       RNA815_9549.4 0 0 8.93 X -
Others 468 0.6     RNA815_5404.2 3.58 −0.18 3.97 X -
       RNA815_13 0 4.85 4.87 X -
  1. The transcripts are classified on the basis of their differential expression profile between samples using a three digit code (the 'Class'). Higher than two-fold differences in log2-expression level were considered indicative of differential expression (see Methods). Each digit in the code refers to the comparison between two adjacent samples (i.e. [B vs. A, C vs. B, D vs. C]) with the following coding: positive differential expression (+), no differential expression (0) or negative differential expression (−). The classes correspond to the predicted expression in different organs and body regions. We also give the number (n) and percentage (%) of transcripts in each class and the class mean difference in log2-expression between samples (Mean B-A, Mean C-B, Mean D-C). Furthermore, we give the accession codes of the selected candidate transcripts belonging to different classes (Candidates), the transcript difference in log2-expression between samples (B-A, C-B, D-C), and the summary of the in situ hybridization (ISH) and RNA interference (RNAi) screens, namely expression or phenotype detected (X) or non-detected (−)