| Literature DB >> 31688915 |
Pau Erola1,2, Johan L M Björkegren3,4, Tom Michoel1,5.
Abstract
MOTIVATION: Recently, it has become feasible to generate large-scale, multi-tissue gene expression data, where expression profiles are obtained from multiple tissues or organs sampled from dozens to hundreds of individuals. When traditional clustering methods are applied to this type of data, important information is lost, because they either require all tissues to be analyzed independently, ignoring dependencies and similarities between tissues, or to merge tissues in a single, monolithic dataset, ignoring individual characteristics of tissues.Entities:
Mesh:
Year: 2020 PMID: 31688915 PMCID: PMC7162352 DOI: 10.1093/bioinformatics/btz805
Source DB: PubMed Journal: Bioinformatics ISSN: 1367-4803 Impact factor: 6.937
Fig. 1.Fold-change enrichment of tissue PPIs in tissue clusters for four multi-tissue clustering methods and individual single-tissue clustering. RW4—revamp with prior tissue similarities set according to their overall expression correlation, RA—revamp with prior tissue similarities set to zero, VERT—vertical data concatenation, HORIZ—horizontal data concatenation, INDIV—each tissue clustered individually. Each colored bar shows the fold-change overlap of tissue PPIs in clusters for the matching tissue; the black bar shows the fold-change overlap of tissue-shared PPIs in tissue-shared genes of linked clusters. See Section 2 for details. (Color version of this figure is available at Bioinformatics online.)
Fig. 2.Module regulatory network for all seven tissues. Regulators are presented as squares and clusters as circles with size proportional to the number of genes in the cluster. Only the regulators with a score greater than 20 in the regulators task are represented, and we named those with a score above 60. Edges are colored per tissue as per Figure 3, and their width is proportional to the regulator score. (Color version of this figure is available at Bioinformatics online.)
Fig. 3.Network representation of the correlation between the eigengenes, the first principal component of a given module, and relevant CAD phenotypes (squares), aggregated per tissue (circles). Edge width is inversely proportional to the correlation P-value