ArticleBMC bioinformatics2021
A unified framework for the integration of multiple hierarchical clusterings or networks from multi-source data.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
2 citing papers in PubMed, 6 citations in OpenAlex.
- MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms.Nature communications · 2023Article
- Using expression quantitative trait loci data and graph-embedded neural networks to uncover genotype-phenotype interactions.Frontiers in genetics · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIntegrating data from different sources is a recurring question in computational biology. Much effort has been devoted to the integration of data sets of the same type, typically multiple numerical data tables. However, data types are generally heterogeneous: it is a common place to gather data in the form of trees, networks or factorial maps, as these representations all have an appealing visual interpretation that helps to study grouping patterns and interactions between entities. The question we aim to answer in this paper is that of the integration of such representations.
resultsTo this end, we provide a simple procedure to compare data with various types, in particular trees or networks, that relies essentially on two steps: the first step projects the representations into a common coordinate system; the second step then uses a multi-table integration approach to compare the projected data. We rely on efficient and well-known methodologies for each step: the projection step is achieved by retrieving a distance matrix for each representation form and then applying multidimensional scaling to provide a new set of coordinates from all the pairwise distances. The integration step is then achieved by applying a multiple factor analysis to the multiple tables of the new coordinates. This procedure provides tools to integrate and compare data available, for instance, as tree or network structures. Our approach is complementary to kernel methods, traditionally used to answer the same question.
conclusionOur approach is evaluated on simulation and used to analyze two real-world data sets: first, we compare several clusterings for different cell-types obtained from a transcriptomics single-cell data set in mouse embryos; second, we use our procedure to aggregate a multi-table data set from the TCGA breast cancer database, in order to compare several protein networks inferred for different breast cancer subtypes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.