Matlab r2011a

For conductivity analysis, ROIs were drawn on non-fat-suppressed T2-weighted TSE axial image using MATLAB R2011a (Mathworks, Natick, MA, USA), with reference to DCE-MRI. Out of 50 slices of T2-weighted TSE images, slices that cover the whole tumor were selected. Two independent radiologists (D.J.S and S.Y.K with 2 and 10 years of experience, respectively) manually drew ROIs fitting to the tumors on the selected slices of T2-weighted TSE sequence. They were blinded to the clinicopathologic information of the tumor while measuring conductivity. Conductivity was calculated on each pixel, and the mean and maximum values were recorded.
A dedicated software package (Syngo.via, Siemens Medical Solutions, Erlangen, Germany) was used to analyze PET images. Two independent nuclear medicine physicians (H.C and D.K.O with 11 and 5 year of experience, respectively), blinded to the clinicopathologic information of the tumor, measured SUV values. The maximum (SUVmax), mean (SUVmean), and peak (SUVpeak) SUV were calculated in ROIs manually drawn by visual inspection on the area of the breast tumor containing the highest SUV pixel^{14 (link)}. SUVmax is defined as the highest voxel value within the ROI, while SUVpeak is the mean value of radiotracer uptake within the ROI surrounding the pixel with the highest activity^{14 (link)}. SUVmean is the mean value of all voxels within the ROI^{14 (link)}.

Data analyses were executed with Matlab® R2011a software (Mathworks®, Natick, MA USA). Statistical analysis was performed using RStudio® Version 0.98.981 (RStudio Inc.^©, Boston, MA, USA).

A microultrasound examination of the left kidney was performed, and the renal vascular tree was mapped using power Doppler images (Figure 3(a)) acquired with a central frequency of 32 MHz and a PRF of 5 kHz. Renal flow velocity data were obtained placing the sample volume in correspondence of the central segmental artery and acquiring related PW-Doppler images (Figure 3(a)) with a PRF of 9-10 kHz. Peak systolic velocity (PSV) and end-diastolic velocity (EDV) values were manually measured; mean velocity (MV) was obtained from tracing the envelope of the flow signal correspondent to a single cardiac cycle. Renal resistivity index (RI) was calculated as (PSV-EDV)/PSV, while renal pulsatility index (PI) was assessed as (PSV-EDV)/MV.
Cardiac and renal evaluations were obtained with the software provided with the ultrasound equipment (VEVOLab, FUJIFILM VisualSonics Inc., Toronto, Canada). Vascular assessments required a customized images processing approach which was performed using Matlab R2011a (MathWorks Inc., Natick, MA, USA).

Enrichment of transcriptome-wide molecular interaction modules for ASD candidate genes and cell-type-specific genes was assessed using the hypergeometric probability density function (hygepdf) in MATLAB R2011a (The MathWorks, Inc.). The resulting p values were corrected for multiple testing using false discovery rate (FDR). All results reported are the −log10 of FDR-corrected p values, and only p values <0.001 were considered significant.
Gene list were assessed for shared biological pathways by testing for enrichment of gene ontology terms (GO) using DAVID Bioinformatics Resources 6.7 (Huang et al. 2009 (link)). The complete list of expressed genes in this study’s dataset (13,563 genes) was used as the background. Only gene ontology terms with a Benjamini-Hochberg multiple testing-corrected p value <0.01 are presented as significant.