Kaleidoscope: A Bioinformatics Web Application for In Silico Exploration of Omics Data

Author(s): Khaled Alganem, Ali S. Imami, Smita Sahay, Hunter Eby, Taylen O. Arvay, Mackenzie Abel, Xiaolu Zhang, William Brett McIntyre, Jiwon Lee, Christy Au-Yeung, Roshanak Asgariroozbehani, Roshni Panda, Rammohan Shukla, Sinead M. O'Donovan, Margaret Hahn, Jarek Meller, Robert McCullumsmith.

Background: Exploring research questions through in silico analysis of genomic, transcriptomic, and/or proteomics (omics) data is an essential initial phase of understanding the pathophysiology of medical disorders and requires the use of bioinformatics. Currently, numerous publicly available bioinformatics tools present appealing features to facilitate this endeavor; however, applications are constrained by outdated user interfaces that are difficult to use. Thus, a streamlined, user-friendly, data exploration platform is pertinent in effectively investigating medical disorders and treatment options in silico.

Results: We developed an R Shiny web application called Kaleidoscope to address this challenge. The application offers access to several omics databases and bioinformatics tools to analyze these data, allowing users the ease and flexibility to explore research questions in silico. The application is straightforward to use with a unified interface and offers the ability to upload user-defined datasets. We demonstrate the application features such as building protein-protein interaction networks, generating gene expression and enrichment data across cell-subtypes in the brain, and curating the top differentially expressed genes across schizophrenia versus control transcriptomic datasets with a starting query of the DISC1 (Disrupted in schizophrenia 1) gene.

Conclusion: Kaleidoscope provides easy access to several bioinformatics databases under a unified user interface to explore biomedical research questions in silico. Currently, the application focuses on neuropsychiatric disorders; however, with the flexibility of uploading user-defined datasets, the capability of answering biomedical questions surrounding any medical disorder exists. The web application is opensource and freely available at https://cdrl.shinyapps.io/Kaleidoscope/. In conclusion, Kaleidoscope streamlines the process of in silico data exploration and expands the efficient use of omics tools to stakeholders without specific bioinformatics expertise.