Functional coherence and annotation agreement metrics for enzyme families

Tese de doutoramento, Informática (Bioinformática), Universidade de Lisboa, Faculdade de Ciências, 2015A range of methodologies is used to create sequence annotations, from manual curation by specialized curators to several automatic procedures. The multitude of existing annotation methods consequently generates an annotation heterogeneity in terms of coverage and specificity across the biological sequence space. When comparing groups of similar sequences (such as protein families) this heterogeneity can introduce issues regarding the interpretation of the actual functional similarity and the overall functional coherence. A direct path to mitigate these issues is the annotation extension within the protein families under analysis. This thesis postulates that the protein families can be used as knowledgebases for their own annotation extension with the assistance of a proper functional coherence analysis. Therefore, a modular framework for functional coherence analysis and annotation extension in protein families was proposed. The framework includes a proposed module for functional coherence analysis that relies on graph visualization, term enrichment and other statistics. In this work it was implemented and made available as a publicly accessible web application, GRYFUN which can be accessed at http://xldb.di.fc.ul.pt/gryfun/. In addition, four metrics were developed to assess distinct aspects of the coherence and completeness in protein families in conjunction with additional existing metrics. Therefore the use of the complete proposed framework by curators can be regarded as a semi-automatic approach to annotation able to assist with protein annotation extension.Diversas metodologias são usadas para criar anotações em sequências, desde a curação manual por curadores especializados até vários procedimentos automáticos. A multitude de métodos de anotação existentes consequentemente gera heterogeneidade nas anotações em termos de cobertura e especificidade em espaços de sequências biológicas. Ao comparar grupos de sequências semelhantes (tais como famílias proteícas) esta heterogeneidade pode introduzir dificuldades quanto à interpretação da semelhança e coerência funcional nesses grupos. Uma maneira de mitigar essas dificuldades é a extensão da anotação dentro das famílias proteícas em análise. Esta tese postula que famílias proteícas podem ser usadas como bases de conhecimento para a sua própria extensão de anotação através do uso de análises de coerência funcional apropriadas. Portanto, uma framework modular para a análise de coerência funcional e extensão de anotação em famílias proteícas foi proposta. A framework incluí um módulo proposto para a análise de coerência funcional baseado em visualização de grafos, enriquecimento de termos e outras estatísticas. Neste trabalho o módulo foi implementado e disponibilizado como uma aplicação web, GRYFUN que pode ser acedida em http://xldb.di.fc.ul.pt/gryfun/. Adicionalmente, quatro métricas foram desenvolvidas para aferir aspectos distinctos da coerência e completude de anotação em famílias proteícas em conjunção com métricas já existentes. Portanto, o uso da framework completa por curadores, como uma estratégia de anotação semi-automática, é capaz de potenciar a extensão de anotação.Fundação para a Ciência e a Tecnologia (FCT), SFRH/BD/48035/200

Assessment of protein set coherence using functional annotations

12 pages, 5 figures. -- PMID: 18937846 [PubMed].-- PMCID: PMC2588600.-- Additional information available: File 1: Coherence score and significance measures of random sets.- File 2: Functional analysis of 'Module 39' obtained by Pu et al. [37] using various approaches.[Background] Analysis of large-scale experimental datasets frequently produces one or more sets of proteins that are subsequently mined for functional interpretation and validation. To this end, a number of computational methods have been devised that rely on the analysis of functional annotations. Although current methods provide valuable information (e.g. significantly enriched annotations, pairwise functional similarities), they do not specifically measure the degree of homogeneity of a protein set.[Results] In this work we present a method that scores the degree of functional homogeneity, or coherence, of a set of proteins on the basis of the global similarity of their functional annotations. The method uses statistical hypothesis testing to assess the significance of the set in the context of the functional space of a reference set. As such, it can be used as a first step in the validation of sets expected to be homogeneous prior to further functional interpretation.[Conclusions] We evaluate our method by analysing known biologically relevant sets as well as random ones. The known relevant sets comprise macromolecular complexes, cellular components and pathways described for Saccharomyces cerevisiae, which are mostly significantly coherent. Finally, we illustrate the usefulness of our approach for validating ‘functional modules’ obtained from computational analysis of protein-protein interaction networks.Matlab code and supplementary data are available at: http://www.cnb.csic.es/~monica/coherence/This work has been partially funded by the Spanish grants BIO2007-67150-C03-02, S-Gen- 0166/2006, CYTED-505PI0058, TIN2005-5619, PR27/05-13964-BSCH. APM acknowledges the support of the Spanish Ramón y Cajal program.Peer reviewe

Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures

<p>Abstract</p> <p>Background</p> <p>DNA microarray technology allows for the measurement of genome-wide expression patterns. Within the resultant mass of data lies the problem of analyzing and presenting information on this genomic scale, and a first step towards the rapid and comprehensive interpretation of this data is gene clustering with respect to the expression patterns. Classifying genes into clusters can lead to interesting biological insights. In this study, we describe an iterative clustering approach to uncover biologically coherent structures from DNA microarray data based on a novel clustering algorithm EP_GOS_Clust.</p> <p>Results</p> <p>We apply our proposed iterative algorithm to three sets of experimental DNA microarray data from experiments with the yeast <it>Saccharomyces cerevisiae </it>and show that the proposed iterative approach improves biological coherence. Comparison with other clustering techniques suggests that our iterative algorithm provides superior performance with regard to biological coherence. An important consequence of our approach is that an increasing proportion of genes find membership in clusters of high biological coherence and that the average cluster specificity improves.</p> <p>Conclusion</p> <p>The results from these clustering experiments provide a robust basis for extracting motifs and trans-acting factors that determine particular patterns of expression. In addition, the biological coherence of the clusters is iteratively assessed independently of the clustering. Thus, this method will not be severely impacted by functional annotations that are missing, inaccurate, or sparse.</p

Aplicação de técnicas de Clustering ao contexto da Tomada de Decisão em Grupo

Nowadays, decisions made by executives and managers are primarily made in a group. Therefore, group decision-making is a process where a group of people called participants work together to analyze a set of variables, considering and evaluating a set of alternatives to select one or more solutions. There are many problems associated with group decision-making, namely when the participants cannot meet for any reason, ranging from schedule incompatibility to being in different countries with different time zones. To support this process, Group Decision Support Systems (GDSS) evolved to what today we call web-based GDSS. In GDSS, argumentation is ideal since it makes it easier to use justifications and explanations in interactions between decision-makers so they can sustain their opinions. Aspect Based Sentiment Analysis (ABSA) is a subfield of Argument Mining closely related to Natural Language Processing. It intends to classify opinions at the aspect level and identify the elements of an opinion. Applying ABSA techniques to Group Decision Making Context results in the automatic identification of alternatives and criteria, for example. This automatic identification is essential to reduce the time decision-makers take to step themselves up on Group Decision Support Systems and offer them various insights and knowledge on the discussion they are participants. One of these insights can be arguments getting used by the decision-makers about an alternative. Therefore, this dissertation proposes a methodology that uses an unsupervised technique, Clustering, and aims to segment the participants of a discussion based on arguments used so it can produce knowledge from the current information in the GDSS. This methodology can be hosted in a web service that follows a micro-service architecture and utilizes Data Preprocessing and Intra-sentence Segmentation in addition to Clustering to achieve the objectives of the dissertation. Word Embedding is needed when we apply clustering techniques to natural language text to transform the natural language text into vectors usable by the clustering techniques. In addition to Word Embedding, Dimensionality Reduction techniques were tested to improve the results. Maintaining the same Preprocessing steps and varying the chosen Clustering techniques, Word Embedders, and Dimensionality Reduction techniques came up with the best approach. This approach consisted of the KMeans++ clustering technique, using SBERT as the word embedder with UMAP dimensionality reduction, reducing the number of dimensions to 2. This experiment achieved a Silhouette Score of 0.63 with 8 clusters on the baseball dataset, which wielded good cluster results based on their manual review and Wordclouds. The same approach obtained a Silhouette Score of 0.59 with 16 clusters on the car brand dataset, which we used as an approach validation dataset.Atualmente, as decisões tomadas por gestores e executivos são maioritariamente realizadas em grupo. Sendo assim, a tomada de decisão em grupo é um processo no qual um grupo de pessoas denominadas de participantes, atuam em conjunto, analisando um conjunto de variáveis, considerando e avaliando um conjunto de alternativas com o objetivo de selecionar uma ou mais soluções. Existem muitos problemas associados ao processo de tomada de decisão, principalmente quando os participantes não têm possibilidades de se reunirem (Exs.: Os participantes encontramse em diferentes locais, os países onde estão têm fusos horários diferentes, incompatibilidades de agenda, etc.). Para suportar este processo de tomada de decisão, os Sistemas de Apoio à Tomada de Decisão em Grupo (SADG) evoluíram para o que hoje se chamam de Sistemas de Apoio à Tomada de Decisão em Grupo baseados na Web. Num SADG, argumentação é ideal pois facilita a utilização de justificações e explicações nas interações entre decisores para que possam suster as suas opiniões. Aspect Based Sentiment Analysis (ABSA) é uma área de Argument Mining correlacionada com o Processamento de Linguagem Natural. Esta área pretende classificar opiniões ao nível do aspeto da frase e identificar os elementos de uma opinião. Aplicando técnicas de ABSA à Tomada de Decisão em Grupo resulta na identificação automática de alternativas e critérios por exemplo. Esta identificação automática é essencial para reduzir o tempo que os decisores gastam a customizarem-se no SADG e oferece aos mesmos conhecimento e entendimentos sobre a discussão ao qual participam. Um destes entendimentos pode ser os argumentos a serem usados pelos decisores sobre uma alternativa. Assim, esta dissertação propõe uma metodologia que utiliza uma técnica não-supervisionada, Clustering, com o objetivo de segmentar os participantes de uma discussão com base nos argumentos usados pelos mesmos de modo a produzir conhecimento com a informação atual no SADG. Esta metodologia pode ser colocada num serviço web que segue a arquitetura micro serviços e utiliza Preprocessamento de Dados e Segmentação Intra Frase em conjunto com o Clustering para atingir os objetivos desta dissertação. Word Embedding também é necessário para aplicar técnicas de Clustering a texto em linguagem natural para transformar o texto em vetores que possam ser usados pelas técnicas de Clustering. Também Técnicas de Redução de Dimensionalidade também foram testadas de modo a melhorar os resultados. Mantendo os passos de Preprocessamento e variando as técnicas de Clustering, Word Embedder e as técnicas de Redução de Dimensionalidade de modo a encontrar a melhor abordagem. Essa abordagem consiste na utilização da técnica de Clustering KMeans++ com o SBERT como Word Embedder e UMAP como a técnica de redução de dimensionalidade, reduzindo as dimensões iniciais para duas. Esta experiência obteve um Silhouette Score de 0.63 com 8 clusters no dataset de baseball, que resultou em bons resultados de cluster com base na sua revisão manual e visualização dos WordClouds. A mesma abordagem obteve um Silhouette Score de 0.59 com 16 clusters no dataset das marcas de carros, ao qual usamos esse dataset com validação de abordagem

Extracting the abstraction pyramid from complex networks

<p>Abstract</p> <p>Background</p> <p>At present, the organization of system modules is typically limited to either a multilevel hierarchy that describes the "vertical" relationships between modules at different levels (e.g., module A at level two is included in module B at level one), or a single-level graph that represents the "horizontal" relationships among modules (e.g., genetic interactions between module A and module B). Both types of organizations fail to provide a broader and deeper view of the complex systems that arise from an integration of vertical and horizontal relationships.</p> <p>Results</p> <p>We propose a complex network analysis tool, Pyramabs, which was developed to integrate vertical and horizontal relationships and extract information at various granularities to create a pyramid from a complex system of interacting objects. The pyramid depicts the nested structure implied in a complex system, and shows the vertical relationships between abstract networks at different levels. In addition, at each level the abstract network of modules, which are connected by weighted links, represents the modules' horizontal relationships. We first tested Pyramabs on hierarchical random networks to verify its ability to find the module organization pre-embedded in the networks. We later tested it on a protein-protein interaction (PPI) network and a metabolic network. According to Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), the vertical relationships identified from the PPI and metabolic pathways correctly characterized the <it>inclusion </it>(i.e., <it>part-of</it>) relationship, and the horizontal relationships provided a good indication of the functional closeness between modules. Our experiments with Pyramabs demonstrated its ability to perform knowledge mining in complex systems.</p> <p>Conclusions</p> <p>Networks are a flexible and convenient method of representing interactions in a complex system, and an increasing amount of information in real-world situations is described by complex networks. We considered the analysis of a complex network as an iterative process for extracting meaningful information at multiple granularities from a system of interacting objects. The quality of the interpretation of the networks depends on the completeness and expressiveness of the extracted knowledge representations. Pyramabs was designed to interpret a complex network through a disclosure of a pyramid of abstractions. The abstraction pyramid is a new knowledge representation that combines vertical and horizontal viewpoints at different degrees of abstraction. Interpretations in this form are more accurate and more meaningful than multilevel dendrograms or single-level graphs. Pyramabs can be accessed at <url>http://140.113.166.165/pyramabs.php/</url>.</p

A direct comparison of protein interaction confidence assignment schemes

BACKGROUND: Recent technological advances have enabled high-throughput measurements of protein-protein interactions in the cell, producing large protein interaction networks for various species at an ever-growing pace. However, common technologies like yeast two-hybrid may experience high rates of false positive detection. To combat false positive discoveries, a number of different methods have been recently developed that associate confidence scores with protein interactions. Here, we perform a rigorous comparative analysis and performance assessment among these different methods. RESULTS: We measure the extent to which each set of confidence scores correlates with similarity of the interacting proteins in terms of function, expression, pattern of sequence conservation, and homology to interacting proteins in other species. We also employ a new metric, the Signal-to-Noise Ratio of protein complexes embedded in each network, to assess the power of the different methods. Seven confidence assignment schemes, including those of Bader et al., Deane et al., Deng et al., Sharan et al., and Qi et al., are compared in this work. CONCLUSION: Although the performance of each assignment scheme varies depending on the particular metric used for assessment, we observe that Deng et al. yields the best performance overall (in three out of four viable measures). Importantly, we also find that utilizing any of the probability assignment schemes is always more beneficial than assuming all observed interactions to be true or equally likely

Human protein function prediction: application of machine learning for integration of heterogeneous data sources

Experimental characterisation of protein cellular function can be prohibitively expensive and take years to complete. To address this problem, this thesis focuses on the development of computational approaches to predict function from sequence. For sequences with well characterised close relatives, annotation is trivial, orphans or distant homologues present a greater challenge. The use of a feature based method employing ensemble support vector machines to predict individual Gene Ontology classes is investigated. It is found that different combinations of feature inputs are required to recognise different functions. Although the approach is applicable to any human protein sequence, it is restricted to broadly descriptive functions. The method is well suited to prioritisation of candidate functions for novel proteins rather than to make highly accurate class assignments. Signatures of common function can be derived from different biological characteristics; interactions and binding events as well as expression behaviour. To investigate the hypothesis that common function can be derived from expression information, public domain human microarray datasets are assembled. The questions of how best to integrate these datasets and derive features that are useful in function prediction are addressed. Both co-expression and abundance information is represented between and within experiments and investigated for correlation with function. It is found that features derived from expression data serve as a weak but significant signal for recognising functions. This signal is stronger for biological processes than molecular function categories and independent of homology information. The protein domain has historically been coined as a modular evolutionary unit of protein function. The occurrence of domains that can be linked by ancestral fusion events serves as a signal for domain-domain interactions. To exploit this information for function prediction, novel domain architecture and fused architecture scores are developed. Architecture scores rather than single domain scores correlate more strongly with function, and both architecture and fusion scores correlate more strongly with molecular functions than biological processes. The final study details the development of a novel heterogeneous function prediction approach designed to target the annotation of both homologous and non-homologous proteins. Support vector regression is used to combine pair-wise sequence features with expression scores and domain architecture scores to rank protein pairs in terms of their functional similarities. The target of the regression models represents the continuum of protein function space empirically derived from the Gene Ontology molecular function and biological process graphs. The merit and performance of the approach is demonstrated using homologous and non-homologous test datasets and significantly improves upon classical nearest neighbour annotation transfer by sequence methods. The final model represents a method that achieves a compromise between high specificity and sensitivity for all human proteins regardless of their homology status. It is expected that this strategy will allow for more comprehensive and accurate annotations of the human proteome

Systematic Evaluation of Database Builds in Metaproteomics for the Advancement of Microbiome Research

The microscopic life that inhabits a human shares a unique bond with its host. Microbes perform many functions that are vital to the survival of the human species and have long been shown to regulate the absorption of nutrients and to promote immune function. A lack of exposure to certain microbes early in life, excessive antibiotic usage, and improper diet can perturb human microbiomes and lead to disease. Since the emergence of omic sequencing technologies, it has now become possible to measure and monitor the genes and proteins made by these microorganisms to better understand how they contribute to host health or drive potential disease conditions. Early attempts at studying the genomes and proteomes of these environments have revealed that each person may house a unique community of microbial species, each of which contributes distinct and unique functions that separate healthy vs. disbiotic human gut microbiomes. A subfield of the omics known as metaproteomics is now being used to help characterize all proteins found in an environment, and it has been found to show tremendous potential for describing these microbial systems. However, a great deal remains to be done in this field to improve the accuracy and depth of information gained from these investigations. There is currently no accepted standard for determining which genomic databases are best suitable for searching protein sequencing data and it is difficult to know how/ if false positives are being incorporated into the results. The research for this thesis investigated how database curation affects the number of identified proteins and peptides identified from mice gut metaproteome spectra and explored how functional and taxonomic annotation varied according to the database used. The results indicated that translating a high-depth sequenced and assembled metagenome yielded the highest number of identifications while maintaining a low false discovery rate for mice fecal samples and that each database build identified unique and distinct functional and taxonomic information. The goal of this thesis is to better inform the field of metaproteomics and hopefully guide researchers towards a standard practice of using deep metagenome sequencing for database curation, resulting in more thorough coverage of microbiomes with greater confidence