The RNA world: from experimental laboratory to "in silico" approach. Part 1: User friendly RNA expression databases portals

Tomasz Kolenda; Marianna Śmiełowska; Julia Lipowicz; Julia Ostapowicz; Paula Pacześna; Monika Anna Rosochowicz; Paulina Poter; Joanna Kozłowska-Masłoń; Kacper Guglas; Klaudia Dudek; Nina Grzejda; Katarzyna Regulska; Anna Florczak; Urszula Kazimierczak; Katarzyna Lamperska; Anna Teresiak

doi:10.5603/rpor.99675

The RNA world: from experimental laboratory to "in silico" approach. Part 1: User friendly RNA expression databases portals

Rep Pract Oncol Radiother. 2024 Jun 6;29(2):245-257. doi: 10.5603/rpor.99675. eCollection 2024.

Authors

Tomasz Kolenda^{1

2}, Marianna Śmiełowska³, Julia Lipowicz⁴, Julia Ostapowicz^{5

6}, Paula Pacześna², Monika Anna Rosochowicz^{6

7}, Paulina Poter^{8

9}, Joanna Kozłowska-Masłoń^{1

2

10}, Kacper Guglas^{1

2

11}, Klaudia Dudek^{1

2

12}, Nina Grzejda^{1

2

13}, Katarzyna Regulska^{2

14

15}, Anna Florczak^{16

17}, Urszula Kazimierczak^{16

17}, Katarzyna Lamperska^{1

2}, Anna Teresiak^{1

2}

Affiliations

¹ Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland.
² Greater Poland Cancer Center, Research and Implementation Unit, Poznan, Poland.
³ Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
⁴ Department of Histology and Embryology, Poznan University of Medical Sciences, Poznan, Poland.
⁵ Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland.
⁶ Radiobiology Laboratory, Department of Medical Physics, Greater Poland Cancer Centre, Poznan, Poland.
⁷ Department of Orthopaedic and Traumatology, W. Dega University Hospital, University of Medical Sciences, Poznań, Poland.
⁸ Department of Tumor Pathology and Prophylactics, Poznan University of Medical Sciences, Poznan, Poland.
⁹ Department of Tumor Pathology, Greater Poland Cancer Center, Poznan, Poland.
¹⁰ Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
¹¹ Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland.
¹² Poznan University of Life Sciences, Poznan, Poland.
¹³ Adam Mickiewicz University in Poznan, Poznan, Poland.
¹⁴ Pharmacy, Greater Poland Cancer Centre, Poznan, Poland.
¹⁵ Department of Clinical Pharmacy and Biopharmacy, Poznan University of Medical Sciences, Poznan, Poland, Collegium Pharmaceuticum, Poznan, Poland.
¹⁶ Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Poznan, Poland.
¹⁷ Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.

Abstract

Cellular information about "life instruction" is stored, transferred, and modified using different types of RNA molecules. During the last decades, a growing number of RNA data has been generated thanks to the development of microarray chips and next-generation sequencing (NGS) methods. Improvement of bioinformatics contributed to the discovery of many types of new non-coding RNAs (ncRNAs), mostly with regulatory functions that supplemented the knowledge about the world of RNA. All of it, as well as the Human Genome Project (HGP) and the Cancer Genome Atlas (TCGA) project, has resulted in the formation of data storage and analysis portals which are widely used in cancer research and moved science from in vitro to in silico research. In this review we presented and discussed the data storage and analysis portals used by us, such as cBioPortal, UALCAN, ENCORI, and others. During the revision of these sites, we paid attention to data integration, simplicity of analysis, and results visualization, which are important for users without bioinformatic or statistical skills. In our opinion, the RNA analysis online tools will rapidly develop during the next decade and it seems to be a way for personalization of cancer treatment.

Keywords: RNA; TCGA; analysis; biomarkers; cancer; coding- and non-coding RNA; databases.

Publication types

Review