Fig 1.
Schematic diagram of the experimental workflow of this study.
Table 1.
The details of the transcriptome profiles obtained from NCBI GEO DataSets database.
Table 2.
Association analyses between the differentially expressed genes in ASD and the human LINE-1-inserted gene lists.
Table 3.
Association analyses between the differentially expressed genes in ASD phenotypic subgroups and the human LINE-1-inserted gene lists.
Fig 2.
Venn diagram of LINE-1-inserted genes that are differentially expressed in ASD.
The lists of significantly differentially expressed genes with LINE-1 insertions from each transcriptomic study were overlapped with one another. A total of 351 genes were found to be overlapping in at least two studies.
Table 4.
Developmental and neurological diseases significantly associated with dysregulated genes with LINE-1 insertion predicted via IPA.
Table 5.
Canonical pathways significantly associated with dysregulated genes with LINE-1 insertion predicted by the Ingenuity Pathway Analysis (IPA).
Fig 3.
Predicted gene regulatory network of dysregulated genes with LINE-1 insertion predicted via IPA.
The differentially expressed genes with LINE-1 insertion that were identified in multiple studies were used to create gene regulatory networks. The genes present in our dataset (shown in gray) were predicted to interact with one another and were associated with neurological functions known to be associated with ASD.
Fig 4.
Box plot of the overall LINE-1 methylation level (%Cm) between the ASD and sex/age-matched control groups.
P-values were calculated via the two-tailed t-test with Benjamini-Hochberg correction for multiple subgroup comparisons.
Fig 5.
Correlation analysis of LINE-1 methylation and expression in ASD individuals with severe language deficits and sex-/age-matched controls.
The X-axis represents the percentage of LINE-1 methylation. The Y-axis represents the log2 fold change of LINE-1 expression against GAPDH. R2 and P-values were calculated via Spearman’s correlation method.
Fig 6.
Correlation analysis of LINE-1 methylation and the expression of C1orf27 and ARMC8 in ASD individuals with severe language deficits and sex-/age-matched controls.
The X-axis represents the percentage of LINE-1 methylation. The Y-axis represents the log2 fold change of C1orf27/GAPDH and ARMC8/GAPDH. R2 and P-values were calculated via Spearman’s correlation method.