TABLE 4.
Comparison of results from microarrays to results from RNA-Seq for genes whose brain expression was previously identified as associated with voluntary alcohol consumption in the HXB/BXH recombinant inbred rat panel. Correlations were determined using Spearman’s rank correlation and strain mean gene level normalized expression estimates or strain mean transcript level normalized expression estimates and strain mean alcohol consumption values for the gene and transcript correlations, respectively. Genes are ordered by intramodular connectivity in the original microarray-based coexpression module. The number of transcripts identified for each gene in the detected above background transcriptome is shown with its source of identification. The intramodular connectivity values of genes in the candidate module from the previous study (Saba et al., 2015; Saba et al., 2020) are shown, along with their rank within the module.
| Gene symbol | Gene description | From microarray data (Saba et al. (2015), Saba et al. (2020) | From HXB/BXH RNA-Seq data | |||
|---|---|---|---|---|---|---|
| Correlation with alcohol consumption in microarray data [correlation coefficient (p-Value)] | Connectivity-based intramodular connectivity (rank within module) | Number of transcripts identified in HXB/BXH panel in the DABG transcriptome | Number of Ensembl/StringTie/aptardi transcripts | Most significant transcript correlation with alcohol consumption [correlation coefficient (p-value)] | ||
| Lrap | Locus regulating alcohol preference | −0.55 (0.011) | 2.99 (1) | 1 | 0/1/0 | −0.45 (0.042) |
| Ift81 | Intraflagellar transport 81 | −0.43 (0.051) | 2.66 (2) | 3 | 0/1/2 | −0.44 (0.049) |
| Coq5 | Coenzyme Q5, methyltransferase | −0.50 (0.021) | 2.24 (3) | 2 | 1/0/1 | 0.13 (0.59) |
| Txnip | Thioredoxin interacting protein | 0.61 (0.003) | 2.20 (4) | 1 | 1/0/0 | 0.41 (0.068) |
| P2rx4 | Purinergic receptor P2X 4 | −0.63 (0.002) | 2.15 (5) | 2 | 1/1/0 | −0.58 (0.006) |
| Tmem116 | Transmembrane protein 116 | 0.34 (0.133) | 2.00 (6) | 1 | 1/0/0 | 0.52 (0.017) |
| Cfap91 (formerly Maats1) | Cilia and flagella associated protein 91 | −0.56 (0.008) | 1.95 (7) | 2 | 1/0/1 | 0.21 (0.37) |
| GENE_27603 | Unannotated gene | −0.51 (0.021) | 1.74 (8) | Not included in DABG transcriptome | ||