Panomicon: A web-based environment for interactive, visual analysis of multi-omics data

Rodolfo S Allendes Osorio; Johan T Nyström-Persson; Yosui Nojima; Yuji Kosugi; Kenji Mizuguchi; Yayoi Natsume-Kitatani

doi:10.1016/j.heliyon.2020.e04618

Panomicon: A web-based environment for interactive, visual analysis of multi-omics data

Heliyon. 2020 Aug 19;6(8):e04618. doi: 10.1016/j.heliyon.2020.e04618. eCollection 2020 Aug.

Authors

Rodolfo S Allendes Osorio¹, Johan T Nyström-Persson², Yosui Nojima¹, Yuji Kosugi², Kenji Mizuguchi^{1

3}, Yayoi Natsume-Kitatani^{1

4}

Affiliations

¹ Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki-shi, Osaka, 567-0085, Japan.
² Lifematics Ltd., Sanshin Hatchobori bldg. 5F, 2-25-10 Hatchobori, Chuo-ku, Tokyo-to, 104-0032, Japan.
³ Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan.
⁴ Laboratory of In-silico Drug Design, Center of Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki-shi, Osaka, 567-0085, Japan.

Abstract

Multi-omics analyses, combining transcriptomics, genomics, proteomics, and so on, have led to important insights in many areas of biology and medicine. To support these analyses, software that can handle the difficulties associated with multi-omics datasets is crucial. Here, we describe Panomicon, a web-based, interactive analysis environment for multi-omics data. Building on Toxygates, a tool previously created to study single-omics data that features interactive clustering, heatmaps, and user data uploads, Panomicon introduces improvements for the storage and handling of additional omics types, as well as tools for the generation and visualization of interaction networks between different types of omics data. Panomicon is a new type of environment for the collaborative study of multi-omics data, both for users uploading data to our server and for groups wishing to host their own deployment of Panomicon. We demonstrate Panomicon's capabilities by revisiting a microRNA-mRNA interaction networks study in a non-small cell lung cancer dataset.

Keywords: Bioinformatics; Computational biology; Gene interactions; Gene networks; Genetics; Interactive analysis; Lung cancer; Multi-omics; Visualization; microRNA.