18 research outputs found
Nucleotidyl cyclase division into two clusters by the GP system.
<p>Subfigure (a) shows the active site logo for the adenylate cyclase cluster, while (b) shows that for the guanylate cyclase cluster.</p
Most important residues for the two protein kinase clusters produced by the GP system.
<p>Most important residues for the two protein kinase clusters produced by the GP system.</p
Data combinations which yielded the best results for the protein kinases in five runs of the GP system.
<p>Data combinations which yielded the best results for the protein kinases in five runs of the GP system.</p
Comparison of Mutual Information (MI) values for the clusterings obtained by each technique for the studied protein families.
<p>Comparison of Mutual Information (MI) values for the clusterings obtained by each technique for the studied protein families.</p
DUF849 division into seven clusters produced by manually altering ASMCâs hierarchical clustering in [1].
<p>Subfigures (a) through (g) show the active site logos for clusters G1 through G7, respectively.</p
Protein kinase division into two clusters by the GP system.
<p>Subfigure (a) shows the active site logo for the cluster consisting mainly of Ser/Thr kinases, while (b) shows the logo for the cluster of Tyr kinases combined with the EGFR subcluster.</p
Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering
<div><p>As increasingly more genomes are sequenced, the vast majority of proteins may only be annotated computationally, given experimental investigation is extremely costly. This highlights the need for computational methods to determine protein functions quickly and reliably. We believe dividing a protein family into subtypes which share specific functions uncommon to the whole family reduces the function annotation problemâs complexity. Hence, this workâs purpose is to detect isofunctional subfamilies inside a family of unknown function, while identifying differentiating residues. Similarity between protein pairs according to various properties is interpreted as functional similarity evidence. Data are integrated using genetic programming and provided to a spectral clustering algorithm, which creates clusters of similar proteins. The proposed framework was applied to well-known protein families and to a family of unknown function, then compared to ASMC. Results showed our fully automated technique obtained better clusters than ASMC for two families, besides equivalent results for other two, including one whose clusters were manually defined. Clusters produced by our framework showed great correspondence with the known subfamilies, besides being more contrasting than those produced by ASMC. Additionally, for the families whose specificity determining positions are known, such residues were among those our technique considered most important to differentiate a given group. When run with the crotonase and enolase SFLD superfamilies, the results showed great agreement with this gold-standard. Best results consistently involved multiple data types, thus confirming our hypothesis that similarities according to different knowledge domains may be used as functional similarity evidence. Our main contributions are the proposed strategy for selecting and integrating data types, along with the ability to work with noisy and incomplete data; domain knowledge usage for detecting subfamilies in a family with different specificities, thus reducing the complexity of the experimental function characterization problem; and the identification of residues responsible for specificity.</p></div
Data combinations which yielded the best results for the nucleotidyl cyclases in five runs of the GP system.
<p>Data combinations which yielded the best results for the nucleotidyl cyclases in five runs of the GP system.</p
DUF849 division into seven clusters by the GP system.
<p>Subfigures (a) through (g) show the active site logos for clusters I through VII, respectively.</p
Structures used as templates for modeling the SFLD superfamily sequences.
<p>Structures used as templates for modeling the SFLD superfamily sequences.</p