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De novo deletions, but not duplications, in constrained genes were associated with ASD.
Microarray results showed that upregulated genes were associated with an activated immune response.
Most of the repressed genes were associated with light and sugar responses.
Furthermore, we also found that the enriched gene ontologies and pathways for the downregulated genes were associated with transcription.
Large de novo deletions and de novo deletions in constrained genes were associated with ASD case status.
For the Molecular function category, the most highly represented genes were associated with "binding" and "catalytic activity".
GO analyses showed that the enhancer-dependent regulated genes were associated with the modulation of Wnt pathways (Fig. 4b).
Gene ontology and KEGG pathway analysis showed that the upregulated genes were associated with an activated immune response.
The most abundant groups of genes were associated with transport, metabolic process, defense response, and proteolysis.
The Michigan team also discovered that a higher percentage of positively selected genes were associated with disease in humans than in chimps.
In total, 3404 genes were associated with 4390 OMIM syndromes, each of which was described with a list of HPO phenotype terms.
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