Integration of Online Omics-Data Resources for Cancer Research

Abstract

The manifestations of cancerous phenotypes necessitate alterations at different levels of information-flow from genome to proteome. The molecular alterations at different information processing levels serve as the basis for the cancer phenotype to emerge. To understand the underlying mechanisms that drive the acquisition of cancer hallmarks it is required to interrogate cancer cells using multiple levels of information flow represented by different omics-such as genomics, epigenomics, transcriptomics, and proteomics. The advantage of multi-omics data integration comes with a trade-off in the form of an added layer of complexity originating from inherently diverse types of omics-datasets that may pose a challenge to integrate the omics-data in a biologically meaningful manner. The plethora of cancer-specific online omics-data resources, if able to be integrated efficiently and systematically, may facilitate the generation of new biological insights for cancer research. In this review, we provide a comprehensive overview of the online single-and multi-omics resources that are dedicated to cancer. We catalog various online omics-data resources such as The Cancer Genome Atlas (TCGA) along with various TCGA-associated data portals and tools for multi-omics analysis and visualization, the International Cancer Genome Consortium (ICGC), Catalogue of Somatic Mutations in Cancer (COSMIC), The Pathology Atlas, Gene Expression Omnibus (GEO), and PRoteomics IDEntifications (PRIDE). By comparing the strengths and limitations of the respective online resources, we aim to highlight the current biological and technological challenges and possible strategies to overcome these challenges. We outline the available schemes for the integration of the multi-omics dimensions for stratifying cancer patients and biomarker prediction based on the integrated molecular-signatures of cancer. Finally, we propose the multi-omics driven systems-biology approaches to realize the potential of precision onco-medicine as the

Omics in Systems Biology: Current Progress and Future Outlook

“…For those interested in greater details, they are encouraged to visit the sites listed or read a number of excellent reviews on databases for accessing and analyzing multi‐omic datasets. [ 110–115 ]…”

Proteomics, Personalized Medicine and Cancer

“…Bioinformatics plays a central role in the downstream analysis of the large body of proteomics data that is currently being generated, and as such it is one of the 4 HUPO resource pillars [ 11 ]. A number of iterative bioinformatic tools and web servers have been developed to assist in this analysis [ 84 , 85 ], some targeted specifically for cancer (e.g., Perseus [ 86 ] and the Cancer Genome Atlas (TCGA) [ 87 ]).…”

Human Organoid and Supporting Technologies for Cancer and Toxicological Research

“…Single-cell RNA sequencing technology is especially suitable to patient-derived organoids because it preserves the heterogeneity of the cells (Camp and Treutlein, 2017;Camp et al, 2018). Single-cell level analysis spans not only transcriptome sequencing but also whole-genome, proteome, and metabolome analysis (Irish et al, 2006;Restrepo-Pérez et al, 2018;Das et al, 2020;Xing et al, 2020;Specht et al, 2021). These single-cell level multi-omics analyses have good compatibility with organoid technology.…”