Predicting cross-tissue hormone-gene relations usingbalanced word embeddings

Abstract

MotivationLarge volumes of biomedical literature present an opportunity to build whole-body human models comprising both within-tissue and across-tissue interactions among genes. Current studies have mostly focused on identifying within-tissue or tissue-agnostic associations, with a heavy emphasis on associations among disease, genes and drugs. Literature mining studies that extract relations pertaining to inter-tissue communication, such as between genes and hormones, are solely missing. ResultsWe present here a first study to identify from literature the genes involved in inter-tissue signaling via a hormone in the human body. Our models BioEmbedS and BioEmbedS-TS respectively predict if a hormone-gene pair is associated or not, and whether an associated gene is involved in the hormones production or response. Our models are classifiers trained on word embeddings that we had carefully balanced across different strata of the training data such as across production vs. response genes of a hormone (or) well-studied vs. poorly-represented hormones in the literature. Model training and evaluation are enabled by a unified dataset called HGv1 of ground-truth associations between genes and known endocrine hormones that we had compiled. Our models not only recapitulate known gene mediators of tissue-tissue signaling (e.g., at average 70.4% accuracy for BioEmbedS), but also predicts novel genes involved in inter-tissue communication in humans. Furthermore, the species-agnostic nature of our ground-truth HGv1 data and our predictive modeling approach, demonstrated concretely using human data and generalized to mouse, hold much promise for future work on elucidating inter-tissue signaling in other multi-cellular organisms. AvailabilityProposed HGv1 dataset along with our models predictions, and the associated code to reproduce this work are available respectively at https://cross-tissue-signaling.herokuapp.com/, and https://github.com/BIRDSgroup/BioEmbedS. Contactnmanik@cse.iitm.ac.in