Pathway analysis has been widely used to detect pathways and functions associated with complex disease phenotypes. The proliferation of this approach is due to better interpretability of its results and its higher statistical power compared with the gene-level statistics. A plethora of pathway analysis methods that utilize multi-omics setup, rather than just transcriptomics or proteomics, have recently been developed to discover novel pathways and biomarkers. Since multi-omics gives multiple views into the same problem, different approaches are employed in aggregating these views into a comprehensive biological context. As a result, a variety of novel hypotheses regarding disease ideation and treatment targets can be formulated. In this article, we review 32 such pathway analysis methods developed for multi-omics and multi-cohort data. We discuss their availability and implementation, assumptions, supported omics types and databases, pathway analysis techniques and integration strategies. A comprehensive assessment of each method’s practicality, and a thorough discussion of the strengths and drawbacks of each technique will be provided. The main objective of this survey is to provide a thorough examination of existing methods to assist potential users and researchers in selecting suitable tools for their data and analysis purposes, while highlighting outstanding challenges in the field that remain to be addressed for future development.
Two-dimensional UV spectroscopy: a new insight into the structure and dynamics of biomolecules
Two-dimensional (2D) spectroscopy, originally developed for nuclear magnetic resonance, has been recently extended to the infrared and visible regimes. In this technique sequences of femtosecond light pulses are used to interrogate molecular systems and show, by a double Fourier transform, the correlation between excitation and detection frequencies. Extension to the ultraviolet (UV) regime is of great interest and promises to deliver rich structural and dynamical information on biomolecules such as DNA and proteins; however, it must overcome significant technical challenges. This review summarizes the current development status of 2DUV spectroscopy. After discussing the scientific case for the technique, we introduce its basic principles and review its experimental implementations, as well as the computational tools that have been developed to model the experiments. We conclude by giving a few application examples, which highlight the potential of 2DUV spectroscopy and motivate its further development.
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- Award ID(s):
- 1663822
- NSF-PAR ID:
- 10174888
- Date Published:
- Journal Name:
- Chemical Science
- Volume:
- 10
- Issue:
- 43
- ISSN:
- 2041-6520
- Page Range / eLocation ID:
- 9907 to 9921
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/C9SC03871J
