Dataset Information

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.

ABSTRACT: BACKGROUND:The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links. RESULTS:We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2×10-16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime. CONCLUSIONS:ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster.

SUBMITTER: Nguyen ND

PROVIDER: S-EPMC6936142 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.

Nguyen Nam D ND Blaby Ian K IK Wang Daifeng D

BMC genomics 20191230 Suppl 12

<h4>Background</h4>The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of ...[more]

PMID: 31888454

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Project description:Can dreams reveal insight into our cognitive abilities and aptitudes (i.e., "human intelligence")? The relationship between dream production and trait-like cognitive abilities is the foundation of several long-standing theories on the neurocognitive and cognitive-psychological basis of dreaming. However, direct experimental evidence is sparse and remains contentious. On the other hand, recent research has provided compelling evidence demonstrating a link between dream content and new learning, suggesting that dreams reflect memory processing during sleep. It remains to be investigated whether the extent of learning-related dream incorporation (i.e., the semantic similarity between waking experiences and dream content) is related to inter-individual differences in cognitive abilities. The relationship between pre-post sleep memory performance improvements and learning-related dream incorporation was investigated (N = 24) to determine if this relationship could be explained by inter-individual differences in intellectual abilities (e.g., reasoning, short term memory (STM), and verbal abilities). The extent of dream incorporation using a novel and objective method of dream content analysis, employed a computational linguistic approach to measure the semantic relatedness between verbal reports describing the experience on a spatial (e.g., maze navigation) or a motor memory task (e.g., tennis simulator) with subsequent hypnagogic reverie dream reports and waking "daydream" reports, obtained during a daytime nap opportunity. Consistent with previous studies, the extent to which something new was learned was related (r = 0.47) to how richly these novel experiences were incorporated into the content of dreams. This was significant for early (the first 4 dream reports) but not late dreams (the last 4 dream reports). Notably, here, we show for the first time that the extent of this incorporation for early dreams was related (r = 0.41) to inter-individual differences in reasoning abilities. On the other hand, late dream incorporation was related (r = 0.46) to inter-individual differences in verbal abilities. There was no relationship between performance improvements and intellectual abilities, and thus, inter-individual differences in cognitive abilities did not mediate the relationship between performance improvements and dream incorporation; suggesting a direct relationship between reasoning abilities and dream incorporation. This study provides the first evidence that learning-related dream production is related to inter-individual differences in cognitive abilities.

Dataset Information

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.

Publications

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.

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