Figure 1.
The deformed (left) and normal (right) beaks of Beijing-You chickens.
The chicken with a deformed beak had problem with feeding, drinking, and preening and therefore showed lower body weight and poor mental condition.
Table 1.
Gene-specific primers used in qRT-PCR.
Table 2.
Statistics of tag mapping against reference gene and genome sequence of the chicken.
Table 3.
The number of total reference genes and tags.
Figure 2.
Sequencing saturation analysis for RNA from the deformed (A) and normal beak (B).
Figure 3.
Comparison of gene expression between libraries of deformed and normal beak RNA.
Blue dots represent the transcripts with no significant differential expression. Red and green dots represent transcripts more abundant in the test sample and control, respectively. FDR <0.001 and |log2-Ratio| ≧ 1 were used as the thresholds to judge the significance of gene expression difference.
Figure 4.
Distribution of ratios of distinct tag copy number between libraries of deformed and normal beak RNA.
Red region represents the differentially expressed tags with differential expression less than 5-fold. Blue and green region represent the up- and down-regulated tags of more than 5-fold, respectively.
Table 4.
Some extremely differentially expressed genes (|log2-Ratio (deformed beak/normal beak)| ≧ 9).
Figure 5.
Top 10 enrichment cellular components.
The numbers of genes involved in the components are indicated in parentheses.
Figure 6.
The numbers of genes involved in the pathways are indicated in parentheses.
Table 5.
The two most significantly enriched pathways and the involved differentially expressed genes (DEG).
Figure 7.
qRT-PCR of 8 transcripts for validating the DGE results.
The horizontal axis identifies the 8 transcripts examined by qRT-PCR; the vertical axis shows the relative gene expression level in deformed (individuals 1 and 2) versus normal (individuals 3, 4, 5, and 6) beak tissues. The 4 pairs of individuals were all full sibs. The first bar shows the value obtained from DEG using 1 and 6. NPM3 = nucleophosmin/nucleoplasmin 3; LPL = lipoprotein lipase; BMP4 = bone morphogenetic protein 4; SGOL1 = shugoshin-like 1; KRT19 = Keratin 19; sKer = similar to Scale keratin; MMP7 = matrix metalloproteinase 7; MUC = mucin protein.