Table 2.
Pathway analyses of expression quantitative trait loci implicated genes
| Analysis type | Homo sapiensgenes – REFLIST (19,911) | Actual number of autism eQTL genes (140) | Expected number of autism eQTL genes | Autism eQTL genes (over/under) | Autism eQTL genesP | |
|---|---|---|---|---|---|---|
| Thiamine metabolism |
Pathway |
2 |
1 |
0.01 |
+ |
0.01 |
| Nicotinic acetylcholine receptor signaling |
Pathway |
97 |
3 |
0.63 |
+ |
0.03 |
| P53 pathway feedback loops 1 |
Pathway |
7 |
1 |
0.05 |
+ |
0.05 |
| Sensory perception |
Biological process |
708 |
10 |
4.62 |
+ |
0.02 |
| Sensory perception of sound |
Biological process |
123 |
3 |
0.8 |
+ |
0.05 |
| Carbohydrate metabolic process |
Biological process |
952 |
2 |
6.22 |
- |
0.05 |
| Cell motion |
Biological process |
964 |
11 |
6.29 |
+ |
0.05 |
| Cell adhesion |
Biological process |
1333 |
14 |
8.7 |
+ |
0.05 |
| Immune system process |
Biological process |
2628 |
24 |
17.16 |
+ |
0.05 |
| Cell surface receptor linked signal transduction |
Biological process |
2235 |
21 |
14.59 |
+ |
0.05 |
| Structural constituent of ribosome |
Molecular function |
194 |
5 |
1.27 |
+ |
0.009 |
| Hydrolase activity |
Molecular function |
2236 |
8 |
14.6 |
- |
0.4 |
| Receptor activity |
Molecular function |
1808 |
18 |
11.8 |
+ |
0.5 |
| Methyltransferase activity | Molecular function | 132 | 3 | 0.86 | + | 0.05 |
Analyses were conducted using the program PANTHER. All genes (N = 140) regulated by cis or trans acting eQTL were included in analysis to identify over-representation of pathways, biological processes and molecular functions. A reference list (REFLIST) of annotated genes from the Homo sapiens genome (N = 19,911) provided by PANTHER was used as a comparison to the autism eQTL gene list. One hundred and thirty autism eQTL implicated genes were represented in the PANTHER databases, 10 eQTL target genes were not present in the PANTHER accessible databases. The type of pathway, biological process and molecular function showing enrichment among these eQTL targets is provided as is the number of genes annotated to such data in the REFLIST, and in the comparison autism list. Additionally, the number of genes expected in the autism eQTL list, given the number of genes in the REFLIST, is included. The directionality of over- or under-representation in the PANTHER annotation database is included as well as the Bonferroni corrected P-value indicating the statistical significance of the over- or under-representation of the biological process, molecular function or pathway in the autism eQTL gene list. eQTL: expression quantitative trait loci.