Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data

The investigation of the interconnections between the molecular and genetic events that govern biological systems is essential if we are to understand the development of disease and design effective novel treatments. Microarray and next-generation sequencing technologies have the potential to provide this information. However, taking full advantage of these approaches requires that biological connections be made across large quantities of highly heterogeneous genomic datasets. Leveraging the increasingly huge quantities of genomic data in the public domain is fast becoming one of the key challenges in the research community today.We have developed a novel data mining framework that enables researchers to use this growing collection of public high-throughput data to investigate any set of genes or proteins. The connectivity between molecular states across thousands of heterogeneous datasets from microarrays and other genomic platforms is determined through a combination of rank-based enrichment statistics, meta-analyses, and biomedical ontologies. We address data quality concerns through dataset replication and meta-analysis and ensure that the majority of the findings are derived using multiple lines of evidence. As an example of our strategy and the utility of this framework, we apply our data mining approach to explore the biology of brown fat within the context of the thousands of publicly available gene expression datasets.Our work presents a practical strategy for organizing, mining, and correlating global collections of large-scale genomic data to explore normal and disease biology. Using a hypothesis-free approach, we demonstrate how a data-driven analysis across very large collections of genomic data can reveal novel discoveries and evidence to support existing hypothesis

Distinct Molecular Evolutionary Mechanisms Underlie the Functional Diversification of the Wnt and TGFβ Signaling Pathways

The canonical Wnt pathway is one of the oldest and most functionally diverse of animal intercellular signaling pathways. Though much is known about loss-of-function phenotypes for Wnt pathway components in several model organisms, the question of how this pathway achieved its current repertoire of functions has not been addressed. Our phylogenetic analyses of 11 multigene families from five species belonging to distinct phyla, as well as additional analyses employing the 12 Drosophila genomes, suggest frequent gene duplications affecting ligands and receptors as well as co-evolution of new ligand–receptor pairs likely facilitated the expansion of this pathway’s capabilities. Further, several examples of recent gene loss are visible in Drosophila when compared to family members in other phyla. By comparison the TGFβ signaling pathway is characterized by ancient gene duplications of ligands, receptors, and signal transducers with recent duplication events restricted to the vertebrate lineage. Overall, the data suggest that two distinct molecular evolutionary mechanisms can create a functionally diverse developmental signaling pathway. These are the recent dynamic generation of new genes and ligand–receptor interactions as seen in the Wnt pathway and the conservative adaptation of ancient pre-existing genes to new roles as seen in the TGFβ pathway. From a practical perspective, the former mechanism limits the investigator’s ability to transfer knowledge of specific pathway functions across species while the latter facilitates knowledge transfer

The history of the uhu transposable element in the Hawaiian Drosophila

Thesis (Ph. D.)--University of Hawaii at Manoa, 1994.Includes bibliographical references (leaves 160-175)Microfiche.175 leaves, bound ill. 29 cmThe uhu transposable element belongs to the class of elements that have short inverted repeats. It was originally isolated from Drosophila heteroneura, a Hawaiian picture-winged Drosophila endemic to the Island of Hawaii. Biogeographic and DNA sequence divergence data suggest an ancient origin for the uhu element in the Hawaiian Drusophila. Biogeographic data suggests that uhu arose more than 7 million years ago. Sequence divergence data and phylogenetic analysis suggests that uhu was present in a common ancestor of the species. The maximum distance between two isolates suggests that uhu has been in the Hawaiian Drosophila for 20 million years. Using in situ hybridization to polytene chromosomes, the copy number of uhu in the planitibia subgroup and the adiastola subgroups of the Hawaiian Drosophila is found to be higher in the species endemic to the younger islands than in the species endemic to the older islands. This trend is also seen for the loa transposable element in the planitibia subgroup. No complete loa elements are found in D. picticornis from the island of Kauai, while there are 10 to 20 potentially complete copies of loa in the other species. For the uhu element, the percentage of sites that are variable for the presence or absence of uhu is high in the species on the younger islands, while nearly all the sites in D. picticornis are fixed. This would indicate that uhu has more recently been active in the species on the younger islands. Since all of the species are single island endemics, and believed to have evolved on the island, the increase in copy number and evidence for transpositional activity is consistent with the idea that there has been increase in the activity of transposable element associated with a speciation event

Hippo Pathway Phylogenetics Predicts Monoubiquitylation of Salvador and Merlin/Nf2

<div><p>Recently we employed phylogenetics to predict that the cellular interpretation of TGF-β signals is modulated by monoubiquitylation cycles affecting the Smad4 signal transducer/tumor suppressor. This prediction was subsequently validated by experiments in flies, frogs and mammalian cells. Here we apply a phylogenetic approach to the Hippo pathway and predict that two of its signal transducers, Salvador and Merlin/Nf2 (also a tumor suppressor) are regulated by monoubiquitylation. This regulatory mechanism does not lead to protein degradation but instead serves as a highly efficient “off/on” switch when the protein is subsequently deubiquitylated. Overall, our study shows that the creative application of phylogenetics can predict new roles for pathway components and new mechanisms for regulating intercellular signaling pathways.</p> </div

Kibra/Wwc, Expanded/Frmd and Merlin/Nf2 Maximum Likelihood trees.

<p>A) Kibra/Wwc vertebrate topology matches the species tree. Among invertebrates there is a significant cluster of the echinoderm and urochordate that excludes the cephalochordate, a deviation from the species tree. The Bayesian tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051599#pone.0051599.s001" target="_blank">Figure S1G</a>) shows no differences. B) Expanded/Frmd vertebrate topology matches the species tree. <i>M. musculus</i> Frmd1 was found (NP_001191849.1) but excluded since it contains a mutation in the coding region that led it to be classified as a pseudogene. Our data showing this protein is well conserved in humans and chicken suggests that the mutation is a sequence error or belongs to a mutant allele rather than a pseudogene. Among invertebrates the cephalochordate strongly clusters with vertebrates and the echinoderm is an outlier matching the species tree. The Bayesian tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051599#pone.0051599.s001" target="_blank">Figure S1H</a>) shows no differences. C) Merlin/Nf2 vertebrate topology matches the species tree. Among invertebrates, the hemichordate, cephalochordate and echinoderm form a strong cluster without the urochordate, an arrangement that deviates from the species tree. The Bayesian tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051599#pone.0051599.s001" target="_blank">Figure S1I</a>) shows no differences.</p

Overall amino acid substitution rates for families in the Wnt, Hippo and TGF-ß pathways.

a<p>Substitution rate per residue per billion years shown in ascending order by pathway. For each pathway an example of two physically interacting proteins with concordant rates is <u>underlined</u> (e.g., Shaggy/Gsk3 and Axin) and an example of two physically interacting proteins with discordant rates is <b>bold</b> (e.g., Fz and Arrow/Lrp).</p

Warts/Lats and Mats/Mob Maximum Likelihood trees.

<p>A) Warts/Lats vertebrate topology matches the species tree. Among invertebrates, these proteins should be sequentially joined to the vertebrate cluster and thus this part of the Warts/Lats tree deviates from the species tree. The Bayesian tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051599#pone.0051599.s001" target="_blank">Figure S1C</a>) shows one difference - rather than the hemichordate and echinoderm clustering together they are sequentially clustered with the large urochordate, cephalochordate and vertebrate group, an arrangement that better matches the species tree. B) Mats/Mob vertebrate topology matches the species tree except for difficulty resolving human, mouse and chicken Mob1a. Among invertebrates a cluster of the echinoderm and urochordate sequences is attached to the vertebrate cluster with the hemichordate and cephalochordates as outliers. The association of urochordates with vertebrates matches the species tree but the inclusion of echinoderms without hemichordates and cephalochordates does not. The Bayesian tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051599#pone.0051599.s001" target="_blank">Figure S1D</a>) shows one difference - the urochordate switches places with the hemichordate leading to an arrangement that better matches the species tree but with no confidence.</p

Hippo/Mst and Salvador Maximum Likelihood trees.

<p>Trees rooted with <i>D. melanogaster</i> are shown. Branches considered statistically weak (aLRT values <0.70) are colored in blue. Branch lengths are drawn to scale and correspond to the average number of amino acid changes per site as indicated by the scale bar. A) Hippo/Mst vertebrate topology matches the species tree. Among invertebrates the hemichordate strongly clusters with vertebrates while the echinoderm is an outlier. The overall Hippo/Mst tree matches the species tree. The Bayesian tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051599#pone.0051599.s001" target="_blank">Figure S1A</a>) shows one difference - the hemichordate moves out of the strong cluster with vertebrates to become an outlier like the echinoderm. B) Salvador vertebrate topology matches the species tree. Among invertebrates the urochordate clusters tightly with vertebrates while the echinoderm and cephalochordate are outliers. The overall Salvador tree matches the species tree. The Bayesian tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051599#pone.0051599.s001" target="_blank">Figure S1B</a>) shows one difference - the cephalochordate clusters outside the urochordate and vertebrate cluster with confidence.</p