Mouse Pons and Medulla oblongata

For RNAseq, mouse Pons and Medulla oblongata are combined in one sample. Idividual pages for Pons and Medulla oblongata with data of human and pig can be found.

Regionally elevated expression in mouse

Figure 2. Schematic drawing of the mouse brain, indicating the location of pons and medulla from a sagittal view.

The transcriptome analysis shows that 61% (n=12331) of all mouse one-to-one human orthologue genes (n=16320) are expressed in the pons and medulla and 97 genes show an elevated expression in pons and medulla compared to other regions of the brain.

Table 3: Number of genes within the different categories of regionally elevated expression, in mouse pons and medulla

Specificity Number of Mouse elevated genes
Region enriched 36
Group enriched 46
Region enhanced 15
Elevated 97

Elevated expression in pons and medulla compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in pons and medulla compared to all other regions), group enriched (at least four-fold higher mRNA levels in a group of 2-5 regions) and regionally enhanced (at least four-fold higher mRNA levels in pons and medulla compared to the average of all regions), The number of genes in the individual category is shown in Table 3. In Table 4, the 12 genes with the highest level of regional specificity among the 36 enriched genes are listed.

Table 4: The 12 genes with the highest level of enriched expression in mouse pons and medulla. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. RS-score (Regional Specificity score) corresponds to the score calculated as the fold change to the second highest region.

Gene Description Predicted location RS-score
HOXB5 Homeobox B5 Intracellular 230
HOXA5 Homeobox A5 Intracellular 220
HOXB6 Homeobox B6 Intracellular 102
HOXB8 Homeobox B8 Intracellular 65
HOXB7 Homeobox B7 Intracellular 58
HOXA4 Homeobox A4 Intracellular 46
HOXC5 Homeobox C5 Intracellular 46
HOXD4 Homeobox D4 Intracellular 46
HOXB3 Homeobox B3 Intracellular 39
HOXA2 Homeobox A2 Intracellular 36
HOXB4 Homeobox B4 Intracellular 36
HOXD3 Homeobox D3 Intracellular 35


PCP4L1

SLC10A4

CALCA