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

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

Regularized pointwise map recovery from functional correspondence

The concept of using functional maps for representing dense correspondences between deformable shapes has proven to be extremely effective in many applications. However, despite the impact of this framework, the problem of recovering the point-to-point correspondence from a given functional map has received surprisingly little interest. In this paper, we analyse the aforementioned problem and propose a novel method for reconstructing pointwise correspondences from a given functional map. The proposed algorithm phrases the matching problem as a regularized alignment problem of the spectral embeddings of the two shapes. Opposed to established methods, our approach does not require the input shapes to be nearly-isometric, and easily extends to recovering the point-to-point correspondence in part-to-whole shape matching problems. Our numerical experiments demonstrate that the proposed approach leads to a significant improvement in accuracy in several challenging cases