Manifold embedding for understanding mechanisms of transcriptional regulation

In this paper we propose a manifold embedding methodology to integrate heterogeneous sources of genomic data for the purpose of interpretation of transcriptional regulatory phenomena and subsequent visualization. Using the Gata3 gene as an example, we ask if it is possible to determine which genes (or their products) might be potentially involved in its tissue-specific regulation - based on evidence obtained from various available data sources. Our approach is based on co-embedding of genes onto a manifold wherein the proximity of neighbors is influenced by the probability of their interaction as reported from diverse data sources - i.e. the stronger the evidence for that gene-gene interaction, the closer they are.