protein_function


deepNF: Deep network fusion for protein function prediction

Our next meeting will be at 2pm on Feb 26th, in room 4160 of the Discovery building. Our Selected paper is deepNF: Deep network fusion for protein function prediction.
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The abstract is as follows.

The prevalence of high-throughput experimental methods has resulted in an abundance of large-scale molecular and functional interaction networks. The connectivity of these networks provide a rich source of information for inferring functional annotations for genes and proteins. An important challenge has been to develop methods for combining these heterogeneous networks to extract useful protein feature representations for function prediction. Most of the existing approaches for network integration use shallow models that cannot capture complex and highly-nonlinear network structures. Thus, we propose deepNF, a network fusion method based on Multimodal Deep Autoencoders to extract high-level features of proteins from multiple heterogeneous interaction networks. We apply this method to combine STRING networks to construct a common low-dimensional representation containing high-level protein features. We use separate layers for different network types in the early stages of the multimodal autoencoder, later connecting all the layers into a single bottleneck layer from which we extract features to predict protein function. We compare the cross-validation and temporal holdout predictive performance of our method with state-of-the-art methods, including the recently proposed method Mashup. Our results show that our method outperforms previous methods for both human and yeast STRING networks. We also show substantial improvement in the performance of our method in predicting GO terms of varying type and specificity.

 

We welcome all who can join us for this discussion. Feel free to begin that discussion in the comments section below.


Affinity regression predicts the recognition code of nucleic acid–binding proteins 1

Our next meeting will be at 3:00 on February 10th, in room 4160 of the Discovery building. Our Selected paper is Affinity regression predicts the recognition code of nucleic acid–binding proteins.
The abstract is as follows.

Predicting the affinity profiles of nucleic acid–binding proteins directly from the protein sequence is a challenging problem. We present a statistical approach for learning the recognition code of a family of transcription factors or RNA-binding proteins (RBPs) from high-throughput binding data. Our method, called affinity regression, trains on protein binding microarray (PBM) or RNAcompete data to learn an interaction model between proteins and nucleic acids using only protein domain and probe sequences as inputs. When trained on mouse homeodomain PBM profiles, our model correctly identifies residues that confer DNA-binding specificity and accurately predicts binding motifs for an independent set of divergent homeodomains. Similarly, when trained on RNAcompete profiles for diverse RBPs, our model correctly predicts the binding affinities of held-out proteins and identifies key RNA-binding residues, despite the high level of sequence divergence across RBPs. We expect that the method will be broadly applicable to modeling and predicting paired macromolecular interactions in settings where high-throughput affinity data are available.

We welcome all who can join us for this discussion. Feel free to begin that discussion in the comments section below.