Cell type properties of Cliques I & II.

<p>(A) Sections of the sum of expressions of genes in cliques I (left) and II (right) are depicted through the most frontal coronal section of the cerebellum that intersects Nucleus X. The boundaries of the cerebellar cortex and of nucleus X are outlined. (B) The corresponding coronal section of the mouse brain in the Allen Mouse Brain Atlas, Allen Institute for Brain Science <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003128#pcbi.1003128-Allen1" target="_blank">[57]</a>.</p

Expression and anatomical properties of Clique II.

<p>(A) Maximal-intensity projection of the sum of expressions of genes in this clique highlights the cerebellar cortex. (B) The fitting score in the cerebellar cortex is highest among all other brain regions and higher than expected by chance (<i>P</i> = 0.018, based on 100,000 random permutations). Some other regions in the cerebral cortex also show a slight deviation from expression values expected by chance (P<0.05). The brain regions of the ABA at 200 micron resolutions (one dot per region on the figure) are grouped into the following main regions: COR (cerebral cortex), OLF (olfactory areas), Hi (hippocampal region), RHi (Retrohippocampal region), STR (striatum), PAL (pallidum), THA (thalamus), HYP (hypoyhalamus), MID,(midbrain), PON (pons), MED (medulla), CER (cerebellum).</p

Expression and anatomical properties of Clique I.

<p>(A) Maximal-intensity projection of the sum of normalized expressions of genes in this clique highlight regions in the cerebellum. (B) The expression fittings in these regions are higher than expected by chance (P = 0.00002, based on 100,000 random permutations). The brain regions of the ABA at 200 micron resolutions (one dot per region on the figure) are grouped into the following main regions: COR (cerebral cortex), OLF (olfactory areas), Hi (hippocampal region), RHi (Retrohippocampal region), STR (striatum), PAL (pallidum), THA (thalamus), HYP (hypoyhalamus), MID,(midbrain), PON (pons), MED (medulla), CER (cerebellum).</p

Cliques of co-expressed genes.

<p>Venn diagram for the ten cliques of co-expressed genes that are highly enriched with autism genes. For each clique, the following parameters are given: the number of autism genes/number of all genes in the clique, the co-expression threshold (in %) of the clique, and the p-value of the autism gene enrichment (using 100,000 Monte Carlo resampling procedure).</p

Cliques of co-expression genes delineated by co-expressed autism genes.

<p>The 59 cliques of co-expression genes containing ≥2 autism genes identified in our data are listed in the rows together with the minimal co-expression value in the clique, and numbers of autism genes and number of total genes in the clique. A p-value indicates the likelihood of finding this number of autism genes in the clique (based on 100,000 Monte Carlo simulations). The 26 autism genes included in the study are depicted in columns with black and white fillings indicating their presence and absence from a clique respectively.</p

Co-expression characteristics of gene networks.

<p>Distributions of co-expression characteristics are depicted for the autism gene network (Red) and for the 3041 genes in the mouse Allen Brain Atlas database (Blue). (A) Cumulative distribution functions (CDFs). Black arrow indicates the maximal difference between the two CDFs. (B) Average and maximum sizes of connected components for different co-expression thresholds are plotted for the autism gene network (Red) and 1000 randomly generated gene networks of size G = 26 (Cyan).</p