Loci nominally associated with autism from genome-wide analysis show enrichment of brain expression quantitative trait loci but not lymphoblastoid cell line expression quantitative trait loci

Table 2 Pathway analyses of expression quantitative trait loci implicated genes

	Analysis type	Homo sapiens genes – 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.

ISSN: 2040-2392