This repository includes the files for node perturbation and attractor analysis used for analysing the transcriptional network of the DISC1 interactome regulating neuronal migration. The code for node perturbation analysis was adapted from BooleanNet and attractor analysis from BoolNet by Priyadarshini Thirunavukkarasu and Pravesh Parekh at the Multimodal Brain Image Analysis Laboratory (MBIAL), supervised by Dr. John P. John in collaboration with Dr. Akira Sawa and Dr. Koko Ishizuka from Johns Hopkins University, School of Medicine, Baltimore.

Attractor analysis was performed using R 3.4.1 BoolNet 2.1.3 package.

Node perturbation analysis was performed using Python 2.7.11 BooleanNet 1.2.7 package.

The code used for node perturbation analysis is an edited version of an example from BooleanNet

The supplementary figures S03-S34 were generated using matplotlib 1.5.1

The files are organized into the following structure:

There are two types of analyses: node perturbation and attractor analysis. For each analysis, source code is present in the respective folder. FM refers to Functional Module while sim refers to simulation. The *_plot.py files were used for generating supplementary figures S03-S34; create_barh_graphs.m file was used for creating supplementary figures S35-S42.

• Simulation 1 refers to TF activating gene and miRNA expression

• Simulation 2 refers to TF inhibiting gene and miRNA expression

• Simulation 3 refers to TF activating gene and inhibiting miRNA expression

• Simulation 4 refers to TF inhibiting gene and activating miRNA expression

This work is under review. During the review period, if you use any of this work, please contact the authors for citation details.

Title: A novel in silico approach for discovery of microRNA-TF regulation of DISC1 interactome mediating neuronal migration

Authors: John P. John^1,2, Priyadarshini Thirunavukkarasu^1,2, Koko Ishizuka³, Pravesh Parekh^1,2, and Akira Sawa⁴

Affiliations: ¹Multimodal Brain Image Analysis Laboratory (MBIAL); ²Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore 560029, India

³Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA.

⁴Departments of Psychiatry, Mental Health, Neuroscience, and Biomedical Engineering, Johns Hopkins University, School of Medicine, Bloomberg School of Public Health, Baltimore, MD 21287, USA.

Dr. John P. John (jpj@nimhans.ac.in, jpjnimhans@gmail.com)

For code related queries, please contact:

Priyadarshini Thirunavukkarasu: galaxie2485@yahoo.co.in

Pravesh Parekh: praveshparekh@gmail.com