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Table 2 Pathway analyses of expression quantitative trait loci implicated genes

From: 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

  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
  1. 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.