Table 2.
Sex-Specific lncRNAs That Showed Strong Negative Correlations With Sex-Specific Protein Coding Gene Modules of the Opposite Sex Bias and Inverse Hypox-Response Class
| Sex-Specific lncRNAa | Hypox-Response Class of the lncRNA | DO Mouse Liver Data Set Used to Discover Gene Module Showing Negative Correlation | Pearson Correlation Coefficient | Significance of Correlation (FDR) | Sex-Specific Protein-Coding Gene Module | Hypox-Response Class That Shows Enrichment in the Gene Module | Significance of Hypox-Class Enrichment of Gene Module (q value) | No. of Genes in the Module | Overlaps eRNA |
|---|---|---|---|---|---|---|---|---|---|
| ncRNA_inter_chr7_6509 | MC 1 | Female | −0.59 | 1.05E−09 | darkorange | FC 2 | 3.70E−02 | 13 | Yes |
| ncRNA_inter_chr6_5316 | MC 1 | Female | −0.47 | 1.01E−05 | green | FC 2 | 7.13E−05 | 57 | No |
| ncRNA_inter_chr1_630 | MC 1 | Female | −0.45 | 3.82E−05 | green | FC 2 | 7.13E−05 | 57 | No |
| ncRNA_inter_chr8_7423 | MC 1 | Female | −0.44 | 5.70E−05 | green | FC 2 | 7.13E−05 | 57 | Yes |
| ncRNA_inter_chr10_9000 | MC 2 | Female | −0.60 | 3.35E−10 | grey60 | FC 1 | 5.92E−05 | 18 | Yes |
| ncRNA_inter_chr2_1430 | FC 2 | Male | −0.51 | 4.04E−06 | pink | MC 1 | 4.76E−04 | 40 | No |
| ncRNA_inter_chr2_1430 | FC 2 | Male | −0.48 | 1.18E−05 | lightcyan | MC 1 | 1.91E−03 | 23 | No |
| ncRNA_inter_chr10_9222 | FC 2 | Female | −0.47 | 1.01E−05 | skyblue | MC 1 | 2.52E−02 | 12 | No |
| ncRNA_inter_chr3_2937 | FC 2 | Female | −0.54 | 1.27E−07 | greenyellow | MC 1 | 4.41E−05 | 22 | Yes |
Abbreviations: chr, chromosome; FC, female class; inter, intergenic; MC, male class; ncRNA, noncoding RNA.
One of the eight lncRNAs shown (lncRNA_chr2_1430) is negatively correlated with two closely related gene modules (Fig. 4). Furthermore, one female liver gene module (green) is negatively correlated with a total of three lncRNAs. lncRNA_chr8_7423 also showed significant negative correlation with the female hypox-class 2–enriched darkgrey module in male liver (see “Discussion”). Additional details about these eight lncRNAs are provided in Supplemental Table 9C and 9D (44). None of these lncRNAs has annotations in the National Center for Biotechnology Information Reference Sequence database, but four were previously listed in a noncoding RNA database [see Supplemental Table 9C (44)].