Figure 1.
Identification of lncRNA in mouse liver.
(A) Pipeline for gene annotation and identification of lncRNAs. (B) Number of Protein-coding genes and lncRNAs expressed during liver postnatal maturation. *Other non-coding RNAs include Ensembl66 annotated t-RNAs, r-RNAs, miRNAs, snRNAs, snoRNAs, and miscRNAs. **ANOVA was used to test for significant difference in expression during development. P-values were adjusted using Benjamini-Hochberg algorithm with a threshold of 0.05.
Table 1.
Number of expressed protein-coding genes and lncRNAs at each developmental age.
Figure 2.
The similarity of gene expression profiles between any two different ages represented by Pearson Correlation Coefficient for protein-coding + lncRNAs, protein-coding mRNAs alone, and lncRNAs alone.
Figure 3.
Developmental expression of lncRNA n415926 (identified by Noncode v3.0) and its neighbor protein coding gene Cdkn1b.
(A) Sequence read distribution at day −2, 5, 20, and 60 viewed by the UCSC genome browser. (B) Gene expression (represented by FPKM) across the 12 selected ages.
Figure 4.
Developmental expression of antisense lncRNA Gm14198 (identified by Ensembl 66) and its neighbor protein coding gene Zfp341.
(A) Sequence read distribution at day −2, 5, 20, and 60 viewed by the UCSC genome browser. (B) Gene expression (represented by FPKM) across the 12 selected ages.
Figure 5.
Developmental expression of lincRNA Gm16157 (identified by Ensembl 66) and its neighbor protein coding genes Fam169b and Igf1r.
(A) Sequence read distribution at day −2, 5, 30, and 60 viewed by the UCSC genome browser. (B) Gene expression (represented by FPKM) across the 12 selected ages.
Figure 6.
Developmental gene expression patterns during postnatal liver maturation.
Heat maps are drawn for all significantly differentiated expressed protein-coding (A) and lncRNA (B) genes during development in liver. Differential expressions were detected by ANOVA with adjusted p-values <0.05. For each gene, log2(FPKM+1) over the ages were converted to z-scores, and the scale bar indicates z-score values. Genes are hierarchically clustered, and the color bar on the right shows the major trends of gene expression: high relative expression at early ages (neonatal, Cluster 1), intermediate ages (adolescent, Cluster 2) and older ages (adult, Cluster 3). (C). The ideogram of the chromosomal location of genes expressed in the three major developmental patterns.
Figure 7.
Distribution of correlation R value for expression patterns between pairs of neighboring genes.
Random are gene pairs selected at random; PC-PC All means every nearest PC (protein-coding) neighbor for every PC gene; PC-NC All means every nearest PC neighbor for every NC (long non-coding) gene; PC-PC Hi means PC-PC neighbor pairs within 10 kb of each other, and at least one gene in the pair is expressed; PC-NC Hi means PC-NC neighbor pairs within 10 kb of each other, and NC must be expressed. The number of gene pairs in each group is shown in the parenthesis.
Table 2.
Representative GO categories for protein-coding genes with neighboring lncRNAs expressed in the same developmental patterns.