Article: List2Net: Linking multiple lists of biological data in a network context.
Computational and structural biotechnology journal
2023 Volume 23, Page(s) 10–21
Abstract: Motivation: A common task in scientific research is the comparison of lists or sets of diverse biological entities such as biomolecules, ontologies, sequences and expression profiles. Such comparisons rely, one way or another, on calculating a measure ... ...
| Abstract | Motivation: A common task in scientific research is the comparison of lists or sets of diverse biological entities such as biomolecules, ontologies, sequences and expression profiles. Such comparisons rely, one way or another, on calculating a measure of similarity either by means of vector correlation metrics, set operations such as union and intersection, or specific measures to capture, for example, sequence homology. Subsequently, depending on the data type, the results are often visualized using heatmaps, Venn, Euler, or Alluvial diagrams. While most of the abovementioned representations offer simplicity and interpretability, their effectiveness holds only for a limited number of lists and specific data types. Conversely, network representations provide a more versatile approach where data lists are viewed as interconnected nodes, with edges representing pairwise commonality, correlation, or any other similarity metric. Networks can represent an arbitrary number of lists of any data type, offering a holistic perspective and most importantly, enabling analytics for characterizing and discovering novel insights in terms of centralities, clusters and motifs that can exist in such networks. While several tools that implement the translation of lists to the various commonly used diagrams, such as Venn and Euler, have been developed, a similar tool that can parse, analyze the commonalities and generate networks from an arbitrary number of lists of the same or heterogenous content does not exist. Results: To address this gap, we introduce |
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| Language | English |
| Publishing date | 2023-11-14 |
| Publishing country | Netherlands |
| Document type | Journal Article |
| ZDB-ID | 2694435-2 |
| ISSN | 2001-0370 |
| ISSN | 2001-0370 |
| DOI | 10.1016/j.csbj.2023.11.020 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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