Table 6

Global functional analysis: Enrichment of high level functions represented in datasets of differentially expressed genes across 5 sets of monozygotic twins

High level function

Significance(× 102) of enrichment of top five high level functions


Twin sets


361/360

809/810

2369/2368

2595/2596

2597/2598


Nervous system development and function

0.008–3.85 (6/19)*

0.12–2.55 (3/7)

0.81–4.79 (5/33)

0.12–4.39 (12/50)

0.02–4.53 (7/26)

Tissue morphology

0.008–4.27 (8/19)

NA(0/7)

0.81–4.79 (8/33)

0.08–4.38 (18/50)

0.51–4.03 (4/26)

Cell death

0.01–4.27 (8/19)

3.74 (1/7)

0.09–4.79 (4/33)

0.18–4.65 (12/50)

0.09–4.53 (6/26)

Cellular development

0.01–4.27 (6/19)

NA (0/7)

0.81–4.79 (4/33)

0.12–4.39 (8/50)

0.03–3.54 (6/26)

Immune and lymphatic system development and function

0.03–3.85 (9/19)

NA (0/7)

0.81–4.79 (10/33)

0.33–4.39 (17/50)

0.19–4.03 (9/26)


Global functional analysis of differential gene expression across 5 sets of monozygotic autistic twins (each pair identified by blood sample numbers (eg., 361/360) who are discordant with respect to severity of autism or language impairment) was performed using Ingenuity's Pathways Analysis Software.

Significance calculated for each function is an indicator of the likelihood that the high level function is associated with the dataset by random chance. The p-value, which is calculated using the right-tailed Fisher's Exact Test, compares the number of user-specified genes of interest (in this case, differentially expressed genes with a log2(ratio) cutoff ≥ ± 0.58) that participate in a given function or pathway to the total number of occurrences of these genes in all functional/pathway annotations stored in the Ingenuity Pathways Knowledge Base. It is noteworthy that genes related to nervous system development and function rank first among the top 5 out of 74 high level functions identified in lymphoblastoid cell lines on the basis of differentially expressed genes across 5 sets of twins with autism spectrum disorders. The range of significance values for each high level function relates to the different significance values for specific subfunctions within the category.

*(number of differentially expressed genes in functional category/total number of differentially expressed network focus genes with identifiable "high level function" across 5 datasets)

NA: no significance value for this function within the dataset for this pair of twins

Hu et al. BMC Genomics 2006 7:118   doi:10.1186/1471-2164-7-118

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