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Table 3 Summary of differential expression comparisons performed in CLC Genomics Workbench. Expression values were normalised and significant difference ascertained by Baggerley's test, with FDR-corrected p value cutoff at 0.1%. Contigs were selected for up-regulation in males over females, and 3-5h embryos over 2-3h embryos using normalised fold-change.

From: Comprehensive transcriptome analysis of early male and female Bactrocera jarvisi embryos

  Comparison Samples¹ No. of differentially expressed contigs (FDR p < 0.001) No. up-regulated in males and/or older embryos Additional filters No. of transcripts of interest
  Male/Female comparisons      
A Late only (3-5h) 1,2 vs 3,4 2 0   0
B Late only (3-5h), excl. BJ1 2 vs 3,4 21 9 †mean normalised RPKM of female samples <5 5
C Early only (2-3h) 5,6 vs 7,8 73 4 †mean normalised RPKM of female samples <5 0
D Early only (2-3h), excl. BJ5 6 vs 7,8 142 46 †mean normalised RPKM of female samples <5 4
E Both (3-5h and 2-3h) 1,2,5,6 vs 3,4,7,8 0 0   
F Both (3-5h and 2-3h) excl. BJ1 and BJ5 2,6 vs 3,4,7,8 0 0   
G Both (3-5h and 2-3h) excl. BJ1 2,5,6 vs 3,4,7,8 0 0   
  Time comparisons      
H Both (Male and female) 1,2,3,4 vs 5,6,7,8 283 86   
I Both (Male and female) excl. BJ1 and BJ5 2,3,4 vs 6,7,8 2313 1213 #mean normalised RPKM of 2-3h samples <50 1051*
J Both (Male and female) excl. BJ1 2,3,4 vs 5,6,7,8 1846 1128 #mean normalised RPKM of 2-3h samples <50 1019
K Male only 1,2 vs 5,6 14 2   
L Male only excl. BJ1 and BJ5 2 vs 6 1321 827 #mean normalised RPKM of 2-3h samples <50 673*
M Male only excl. BJ2 and BJ6 1 vs 5 183 66   
N Female only 3,4 vs 7,8 1980 862*   
  Intersections      
  I ∩ L      341
  (I ∩ L) - (I ∩ L ∩ N)      105
  1. ¹ Samples BJ1- BJ8 are abbreviated to 1-8
  2. †Allowed extra expression (RPKM<5) in female samples to cover any accidental inclusion of male embryos
  3. # Determined cutoff to be 20% higher than the mean expression, in 2-3h embryos, of sisA, a transcript expressed early in D. melanogaster
  4. *Subsets of I, L and N used in intersections