Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses.

We report an update of the Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including twenty bees, twenty-three ants, eleven wasps and four sawflies. With a reorganized website, HGD continues to provide the HymenopteraMine genomic data mining warehouse and JBrowse/Apollo genome browsers integrated with BLAST. We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt with more than a ten-fold increase in the number of GO-annotated genes. We have also generated orthology datasets that encompass all HGD species and provide orthologue clusters for fourteen taxonomic groups. The new GO annotation and orthology data are available for searching in HymenopteraMine, and as bulk file downloads.

The Human Disease Ontology 2022 update.

The Human Disease Ontology (DO) (www.disease-ontology.org) database, has significantly expanded the disease content and enhanced our userbase and website since the DO's 2018 Nucleic Acids Research DATABASE issue paper. Conservatively, based on available resource statistics, terms from the DO have been annotated to over 1.5 million biomedical data elements and citations, a 10× increase in the past 5 years. The DO, funded as a NHGRI Genomic Resource, plays a key role in disease knowledge organization, representation, and standardization, serving as a reference framework for multiscale biomedical data integration and analysis across thousands of clinical, biomedical and computational research projects and genomic resources around the world. This update reports on the addition of 1,793 new disease terms, a 14% increase of textual definitions and the integration of 22 137 new SubClassOf axioms defining disease to disease connections representing the DO's complex disease classification. The DO's updated website provides multifaceted etiology searching, enhanced documentation and educational resources.

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles.

JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.

Genotyping-By-Sequencing diversity analysis of international Vanilla collections uncovers hidden diversity and enables plant improvement.

Genomics-based diversity analysis of natural vanilla populations is important in order to guide conservation efforts and genetic improvement through plant breeding. Vanilla is a cultivated, undomesticated spice that originated in Mesoamerica prior to spreading globally through vegetative cuttings. Vanilla extract from the commercial species, mainly V. planifolia and V. × tahitensis, is used around the world as an ingredient in foods, beverages, cosmetics, and pharmaceuticals. The global reliance on descendants of a few foundational clones in commercial production has resulted in an industry at heightened risk of catastrophic failure due to extremely narrow genetic diversity. Conversely, national and institutional collections including those near the center of cultivation contain previously undiscovered diversity that could bolster the genetic improvement of vanilla and guide conservation efforts. Towards this goal, an international vanilla genotyping effort generated and analyzed 431,204 single nucleotide polymorphisms among 412 accessions and 27 species from eight collections. Phylogenetic and STRUCTURE analysis sorted vanilla by species and identified hybrid accessions. Principal Component Analysis and the Fixation Index (FST) were used to refine relationships among accessions and showed differentiation among species. Analysis of the commercial species split V. planifolia into three types with all V. × tahitensis accessions being most similar to V. planifolia type 2. Finally, an in-depth analysis of V. × tahitensis identified seven V. planifolia and six V. odorata accessions as most similar to the estimated parental genotypes providing additional data in support of the current hybrid theory. The prevalence of probable V. × tahitensis parental accessions from Belize suggests that V. × tahitensis could have originated from this area and highlights the need for vanilla conservation throughout Central and South America. The genetic groupings among accessions, particularly for V. planifolia, can now be used to focus breeding efforts on fewer accessions that capture the greatest diversity.

Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae.

BACKGROUND: The plastome of medicinal and endangered species in Kingdom of Saudi Arabia, Barleria prionitis was sequenced. The plastome was compared with that of seven Acanthoideae species in order to describe the plastome, spot the microsatellite, assess the dissimilarities within the sampled plastomes and to infer their phylogenetic relationships. RESULTS: The plastome of B. prionitis was 152,217 bp in length with Guanine-Cytosine and Adenine-Thymine content of 38.3 and 61.7% respectively. It is circular and quadripartite in structure and constitute of a large single copy (LSC, 83, 772 bp), small single copy (SSC, 17, 803 bp) and a pair of inverted repeat (IRa and IRb 25, 321 bp each). 131 genes were identified in the plastome out of which 113 are unique and 18 were repeated in IR region. The genome consists of 4 rRNA, 30 tRNA and 80 protein-coding genes. The analysis of long repeat showed all types of repeats were present in the plastome and palindromic has the highest frequency. A total number of 98 SSR were also identified of which mostly were mononucleotide Adenine-Thymine and are located at the non coding regions. Comparative genomic analysis among the plastomes revealed that the pair of the inverted repeat is more conserved than the single copy region. In addition high variation is observed in the intergenic spacer region than the coding region. The genes, ycf1and ndhF and are located at the border junction of the small single copy region and IRb region of all the plastome. The analysis of sequence divergence in the protein coding genes indicates that the following genes undergo positive selection (atpF, petD, psbZ, rpl20, petB, rpl16, rps16, rpoC, rps7, rpl32 and ycf3). Phylogenetic analysis indicated sister relationship between Ruellieae and Justcieae. In addition, Barleria, Justicia and Ruellia are paraphyletic, suggesting that Justiceae, Ruellieae, Andrographideae and Barlerieae should be treated as tribes. CONCLUSIONS: This study sequenced and assembled the first plastome of the taxon Barleria and reported the basics resources for evolutionary studies of B. prionitis and tools for phylogenetic relationship studies within the core Acanthaceae.

The evolving role of cytoreductive nephrectomy: incorporating genomics of metastatic renal cell carcinoma into treatment decisions.

PURPOSE OF REVIEW: Recent publications evaluating cytoreductive nephrectomy in the era of targeted therapy emphasize the importance of patient selection. We reviewed the predictive role of genetic alterations in patients with metastatic renal cell carcinoma (mRCC) undergoing cytoreductive nephrectomy. RECENT FINDINGS: Studies evaluating the association between genetic alterations and outcomes following systemic treatment for mRCC include mainly patients after cytoreductive nephrectomy. Expression of proangiogenic genes, single nucleotide polymorphisms involving genes of the vascular-endothelial growth factor (VEGF) pathway and somatic mutations of chromatin remodeling genes were associated with response to VEGF-targeted therapy. Outcomes following treatment with mammalian target of rapamycin (mTOR) inhibitors were initially associated with mTOR/TSC1/TSC2 mutations; however, subsequent studies did not validate these findings but rather found an association between loss of PTEN expression and PBRM1 mutations and improved outcomes. Loss of PBRM1 was initially linked to response to immunotherapy; however, larger studies question this association and showed high expression of T-effector gene signature predicted improved outcome. Primary tumors with low intratumor heterogeneity but elevated somatic copy-number alterations were associated with rapid progression at multiple sites. SUMMARY: Genetic alterations may help select patients for cytoreductive nephrectomy and optimize timing of treatment. Intratumor heterogeneity and genetic discordance between primary and metastatic tumors may limit clinical applicability. Future studies should evaluate approaches to overcome these limitations.

Primer in Genetics and Genomics, Article 5-Further Defining the Concepts of Genotype and Phenotype and Exploring Genotype-Phenotype Associations.

As nurses begin to incorporate genetic and genomic sciences into clinical practice, education, and research, it is essential that they have a working knowledge of the terms foundational to the science. The first article in this primer series provided brief definitions of the basic terms (e.g., genetics and genomics) and introduced the concept of phenotype during the discussion of Mendelian inheritance. These terms, however, are inconsistently used in publications and conversations, and the linkage between genotype and phenotype requires clarification. The goal of this fifth article in the series is to elucidate these terms, provide an overview of the research methods used to determine genotype-phenotype associations, and discuss their significance to nursing through examples from the current nursing literature.

Design patterns for the development of electronic health record-driven phenotype extraction algorithms.

BACKGROUND: Design patterns, in the context of software development and ontologies, provide generalized approaches and guidance to solving commonly occurring problems, or addressing common situations typically informed by intuition, heuristics and experience. While the biomedical literature contains broad coverage of specific phenotype algorithm implementations, no work to date has attempted to generalize common approaches into design patterns, which may then be distributed to the informatics community to efficiently develop more accurate phenotype algorithms. METHODS: Using phenotyping algorithms stored in the Phenotype KnowledgeBase (PheKB), we conducted an independent iterative review to identify recurrent elements within the algorithm definitions. We extracted and generalized recurrent elements in these algorithms into candidate patterns. The authors then assessed the candidate patterns for validity by group consensus, and annotated them with attributes. RESULTS: A total of 24 electronic Medical Records and Genomics (eMERGE) phenotypes available in PheKB as of 1/25/2013 were downloaded and reviewed. From these, a total of 21 phenotyping patterns were identified, which are available as an online data supplement. CONCLUSIONS: Repeatable patterns within phenotyping algorithms exist, and when codified and cataloged may help to educate both experienced and novice algorithm developers. The dissemination and application of these patterns has the potential to decrease the time to develop algorithms, while improving portability and accuracy.

gsGator: an integrated web platform for cross-species gene set analysis.

BACKGROUND: Gene set analysis (GSA) is useful in deducing biological significance of gene lists using a priori defined gene sets such as gene ontology (GO) or pathways. Phenotypic annotation is sparse for human genes, but is far more abundant for other model organisms such as mouse, fly, and worm. Often, GSA needs to be done highly interactively by combining or modifying gene lists or inspecting gene-gene interactions in a molecular network. DESCRIPTION: We developed gsGator, a web-based platform for functional interpretation of gene sets with useful features such as cross-species GSA, simultaneous analysis of multiple gene sets, and a fully integrated network viewer for visualizing both GSA results and molecular networks. An extensive set of gene annotation information is amassed including GO & pathways, genomic annotations, protein-protein interaction, transcription factor-target (TF-target), miRNA targeting, and phenotype information for various model organisms. By combining the functionalities of Set Creator, Set Operator and Network Navigator, user can perform highly flexible and interactive GSA by creating a new gene list by any combination of existing gene sets (intersection, union and difference) or expanding genes interactively along the molecular networks such as protein-protein interaction and TF-target. We also demonstrate the utility of our interactive and cross-species GSA implemented in gsGator by several usage examples for interpreting genome-wide association study (GWAS) results. gsGator is freely available at http://gsGator.ewha.ac.kr. CONCLUSIONS: Interactive and cross-species GSA in gsGator greatly extends the scope and utility of GSA, leading to novel insights via conserved functional gene modules across different species.

Classification of genomic signals using dynamic time warping.

BACKGROUND: Classification methods of DNA most commonly use comparison of the differences in DNA symbolic records, which requires the global multiple sequence alignment. This solution is often inappropriate, causing a number of imprecisions and requires additional user intervention for exact alignment of the similar segments. The similar segments in DNA represented as a signal are characterized by a similar shape of the curve. The DNA alignment in genomic signals may adjust whole sections not only individual symbols. The dynamic time warping (DTW) is suitable for this purpose and can replace the multiple alignment of symbolic sequences in applications, such as phylogenetic analysis. METHODS: The proposed method is composed of three main parts. The first part represent conversion of symbolic representation of DNA sequences in the form of a string of A,C,G,T symbols to signal representation in the form of cumulated phase of complex components defined for each symbol. Next part represents signals size adjustment realized by standard signal preprocessing methods: median filtration, detrendization and resampling. The final part necessary for genomic signals comparison is position and length alignment of genomic signals by dynamic time warping (DTW). RESULTS: The application of the DTW on set of genomic signals was evaluated in dendrogram construction using cluster analysis. The resulting tree was compared with a classical phylogenetic tree reconstructed using multiple alignment. The classification of genomic signals using the DTW is evolutionary closer to phylogeny of organisms. This method is more resistant to errors in the sequences and less dependent on the number of input sequences. CONCLUSIONS: Classification of genomic signals using dynamic time warping is an adequate variant to phylogenetic analysis using the symbolic DNA sequences alignment; in addition, it is robust, quick and more precise technique.

Detecção de locos de características quantitativas nos cromossomos 1, 2, 3, 12, 14, 15 e X de suínos: características de desempenho / Detection of quantitative trait loci on chromosomes 1, 2, 3, 12, 14, 15, X in pigs: performance characteristics

Mapeou-se quantitative trait loci (QTL) associados a características de desempenho nos cromossomos 1, 2, 3, 12, 14, 15 e X de suínos pertencentes a uma população F2, formada a partir do cruzamento entre dois machos da raça naturalizada brasileira Piau e 18 fêmeas comerciais (Landrace x Large White x Pietrain). O mapa genético de ligação da população foi construído após a genotipagem dos animais para 35 marcadores microssatélites. As estimativas do conteúdo de informação polimórfica indicaram que os marcadores microssatélites foram adequados para as análises de QTL. Os dados foram analisados pelo mapeamento por intervalo usando-se o programa GridQTL. Encontraram-se seis QTL, sendo que o QTL genômico para idade ao abate atingiu a significância de 5% de probabilidade. As informações dos QTL detectados neste estudo são úteis para identificar genes que podem ser usados em conjunto com os métodos convencionais de seleção, aumentar a acurácia deles e prover uma compreensão dos fenótipos produtivos de suínos.

The accomplishment of the present study had the objective of mapping Quantitative Trait Loci (QTL) related to performance traits in a F2 pig population developed by mating two Brazilian Piau breed sires with 18 dams from a commercial line (Landrace × Large White × Pietrain). The linkage map for this population was constructed after genotyping the animals for 35 microsatellite markers. Estimates of polymorphic information content indicated that the microsatellite markers were appropriate for QTL analyses. The genotypes were analyzed by interval mapping using the GridQTL program. A total of six QTL were found, of which the QTL for slaughter age (days) was significant at the 5% genome-wise level. The information of the significant QTL detected in this study is useful for future fine-mapping studies for the identification of genes. Such information can be used together with traditional methods in breeding programs or even for a better understanding of the phenotypes of swine production.

Rol del sistema de genes CLOCK en las alteraciones del ritmo circadiano en pacientes con Trastorno Bipolar. Estudio de asociación genómica amplia / Role of CLOCK Genes in Circadian Rhythm Alterations, in Patients with Bipolar Disorder. Genome-wide Association Study

Introducción: Las anomalías del ritmo circadiano en el transcurso del TB ha motivado la búsqueda de anomalías en los genes CLOCK asociados a la génesis de ritmos circadianos que podrían estar involucrados en este aspecto de la compleja patología del TB. A pesar de ingentes búsquedas, no se han registrado hallazgos significativos en estudios de asociación amplia de genoma (GWAS/genome-wide association studies). Hay por lo menos 3 razones para explicar estos resultados negativos. En primer lugar el hecho de que los rasgos genéticos de patologías complejas, como es el caso del TB, son habitualmente poligénicos. En segundo término, la organización del reloj/es circadiano/s es bastante más compleja de lo que habitualmente se está dispuesto a admitir; y en tercer lugar, el riesgo genético para TB podría ser compartido entre varias patologías diferentes. Objetivos. Investigar la posibilidad de una asociación entre anomalías en las agrupaciones genéticas responsables de la generación de ritmos circadianos y TB, para lo cual se analizaron las redes constitutivas de los genes CLOCK en por lo menos tres niveles: 1) los genes CLOCK centrales, 2) los genes moduladores de genes CLOCK centrales y 3) los genes controlados por los genes CLOCK centrales. Método: Mediante el uso de método de asociación amplia de genoma con umbrales permisivos se intentó establecer asociaciones significativas entre genes CLOCK y TB comparados con genes control, ademas de incluir asociaciones significativas entre genes CLOCK y TB comparados con genes control, además de incluir asociaciones con otras enfermedades que comparten rasgos clínicos y/o genéticos con el TB, como la Depresión Mayor (DM), Esquizofrenia (E), Trastorno por Déficit de Atención e Hiperactividad (TDAH). Luego de establecer estas asociaciones se compararon los resultados con un conjunto de genes sensibles al litio (Li) y otro grupo sensible a valproato (VPO). Las asociaciones entre TEB y respuesta al litio y/o valproato ...

Introduction. Circadian rythm abnormalities during bipolar disoder has prompetd the search for alterations in CLOCK genes responible for generating circadian rythms, which could be envolved with this complex issue of biipolar disorder. In spite of urgent search, no sinificative results ave been reached in genome wide association scales studies (GWAS). At least three rehaznos could account for this fact: first, genetic traits of complex pathology are usually poligenic, second circadian clock organization is far more complex than usually admitted, and third bipolar disorder genetic risk could be shared with other different diseases. Goals. Search for the possibiity of an association between genetic assemblies anormalies responsible for circadian clock rhythm generation and bipolar disorder. Whith that objective, CLOCK genes networks were analyzed n at least three levels: 1) central CLOCK genes, 2) central CLOCK genes modulators and 3) central CLOCK controlled genes. Method. Using GWAS with permissive tresholds and control comparison, a significative association between CLOCK genes and bipolar disorder was searched, including involvement with other diseases that share common (ADHD). After establishing these associations, results were compared for Lithium and valproate sensitive genes associations. Associations between bipolar disorder, CLOCK genes, lithium and valproate sensitive genes were enriched through comparisons with rhythmic, weakly rhythmic and arrhythmic genes. Results. Significative enrichments were found between CLOCK central genes, bipolar disorder and lithium and valproate sensitive genes, not incluiding CLOCK genes modulators. Associations between bipolar disorder, lithium and valproate sensitive genes and rhythmic genes also were significative, excluding weakly rhythmic and arrhythmic genes. GWAS analysis with flexible tresholds made possible the regognition of association between central CLOCK genes and bipolar disorder, identifying candidate ..

Rol del sistema de genes CLOCK en las alteraciones del ritmo circadiano en pacientes con Trastorno Bipolar. Estudio de asociación genómica amplia / Role of CLOCK Genes in Circadian Rhythm Alterations, in Patients with Bipolar Disorder. Genome-wide Association Study

Introducción: Las anomalías del ritmo circadiano en el transcurso del TB ha motivado la búsqueda de anomalías en los genes CLOCK asociados a la génesis de ritmos circadianos que podrían estar involucrados en este aspecto de la compleja patología del TB. A pesar de ingentes búsquedas, no se han registrado hallazgos significativos en estudios de asociación amplia de genoma (GWAS/genome-wide association studies). Hay por lo menos 3 razones para explicar estos resultados negativos. En primer lugar el hecho de que los rasgos genéticos de patologías complejas, como es el caso del TB, son habitualmente poligénicos. En segundo término, la organización del reloj/es circadiano/s es bastante más compleja de lo que habitualmente se está dispuesto a admitir; y en tercer lugar, el riesgo genético para TB podría ser compartido entre varias patologías diferentes. Objetivos. Investigar la posibilidad de una asociación entre anomalías en las agrupaciones genéticas responsables de la generación de ritmos circadianos y TB, para lo cual se analizaron las redes constitutivas de los genes CLOCK en por lo menos tres niveles: 1) los genes CLOCK centrales, 2) los genes moduladores de genes CLOCK centrales y 3) los genes controlados por los genes CLOCK centrales. Método: Mediante el uso de método de asociación amplia de genoma con umbrales permisivos se intentó establecer asociaciones significativas entre genes CLOCK y TB comparados con genes control, ademas de incluir asociaciones significativas entre genes CLOCK y TB comparados con genes control, además de incluir asociaciones con otras enfermedades que comparten rasgos clínicos y/o genéticos con el TB, como la Depresión Mayor (DM), Esquizofrenia (E), Trastorno por Déficit de Atención e Hiperactividad (TDAH). Luego de establecer estas asociaciones se compararon los resultados con un conjunto de genes sensibles al litio (Li) y otro grupo sensible a valproato (VPO). Las asociaciones entre TEB y respuesta al litio y/o valproato ...(AU)

Introduction. Circadian rythm abnormalities during bipolar disoder has prompetd the search for alterations in CLOCK genes responible for generating circadian rythms, which could be envolved with this complex issue of biipolar disorder. In spite of urgent search, no sinificative results ave been reached in genome wide association scales studies (GWAS). At least three rehaznos could account for this fact: first, genetic traits of complex pathology are usually poligenic, second circadian clock organization is far more complex than usually admitted, and third bipolar disorder genetic risk could be shared with other different diseases. Goals. Search for the possibiity of an association between genetic assemblies anormalies responsible for circadian clock rhythm generation and bipolar disorder. Whith that objective, CLOCK genes networks were analyzed n at least three levels: 1) central CLOCK genes, 2) central CLOCK genes modulators and 3) central CLOCK controlled genes. Method. Using GWAS with permissive tresholds and control comparison, a significative association between CLOCK genes and bipolar disorder was searched, including involvement with other diseases that share common (ADHD). After establishing these associations, results were compared for Lithium and valproate sensitive genes associations. Associations between bipolar disorder, CLOCK genes, lithium and valproate sensitive genes were enriched through comparisons with rhythmic, weakly rhythmic and arrhythmic genes. Results. Significative enrichments were found between CLOCK central genes, bipolar disorder and lithium and valproate sensitive genes, not incluiding CLOCK genes modulators. Associations between bipolar disorder, lithium and valproate sensitive genes and rhythmic genes also were significative, excluding weakly rhythmic and arrhythmic genes. GWAS analysis with flexible tresholds made possible the regognition of association between central CLOCK genes and bipolar disorder, identifying candidate .. (AU)

Modelagem conceitual do sistema de banco de dados ProteinWorldDB / Conceptual modeling of the database system ProteinWorldDB

Esta tese descreve o projeto conceitual do sistema de banco de dados ProteinWorldDB (PWDB). Um ponto importante da proposta do PWDB é permitir a construção de consultas e procedimentos no domínio da genômica comparativa sem a necessidade de comparação de sequências. Além disso, o PCG comparou milhões de sequências de proteína, incluindo o conjunto proteico total de centenas de genomas completos, utilizando programação dinâmica, e não um método heurístico, para os cálculos de similaridade. A estratégia do PCG, assim como a genômica, está fundamentada no conhecimento de que sequências biológicas por si só são pouco informativas; elas precisam ser analisadas a partir de um enfoque comparativo para a inferência de homologia. A comparação de sequências de diferentes organismos introduz uma perspectiva evolutiva ao processo, e o estudo comparativo de genomas completos pode ampliar a escala do conhecimento de um único processo biológico para o de sistemas biológicos complexos em células e organismos. Para responder eficientemente questões dessa natureza, o esquema conceitual apresentado associa bases de dados biológicos de referência aos índices de similaridade já pré-calculados e armazenados pelo PCGUtilizando um formato gráfico de fácil compreensão para representar conceitos e relacionamentos (diagrama ER), o esquema foi proposto para facilitar o planejamento de consultas e procedimentos por pesquisadores da área de genômica (sem conhecimento de linguagens de bancos de dados), assim como guiar o desenvolvimento e a implementação física do PWDB por profissionais da área de computação. Alguns exemplos são apresentados com o objetivo de demonstrar a utilização do esquema conceitual para a especificação de consultas e procedimentos, mesmo antes da existência de um esquema lógico...

This thesis describes the conceptual design of the database system ProteinWorldDB(PWDB). An important point of the PWDB proposal is to allow the construction of queriesand procedures in the field of comparative genomics without the need for sequencecomparison. Moreover, the PCG compared millions of protein sequences, including theentire set of proteins from hundreds of complete genomes using dynamic programming,rather than a heuristic method, for calculating similarityPCG‘s strategy, like that of genomic studies in general, is grounded in the knowledgethat biological sequences alone are uninformative. They need to be analyzed from acomparative approach to infer homology. The comparison of sequences from differentorganisms introduces an evolutionary perspective to the process and the comparativestudy of complete genomes can expand our knowledge from a single biological processall the way to complex biological systems in cells and organisms. To efficiently answerquestions of this nature, the conceptual schema links selected international referencebiological databases to similarity indexes already precomputed and stored by the PCG.By using an easily understandable graphic format to represent concepts andrelationships (ER diagram), the schema was proposed to help the design of queries andprocedures by genomic researchers (who may not have knowledge of databaselanguages) as well as to guide the development and physical implementation of thesystem by developers. Some examples are presented to demonstrate the use of theconceptual schema for specifying queries and procedures, even before the existence ofa logical schema. The schema can be easily extended. Additional modules can be inserted/removed toinclude other protein sequences comparisons projects that may benefit from theinformation provided by the schema´s central module. Likewise, new databases specificto different areas (-omics, for example) can be cross-referenced to the schema...

Rotation of random forests for genomic and proteomic classification problems.

Random Forests have been recently widely used for different kinds of classification problems. One of them is classification of gene expression samples that is known as a problem with extremely high dimensionality, and therefore demands suited classification techniques. Due to its strong robustness with respect to large feature sets, Random Forests show significant increase of accuracy in comparison to other ensemble-based classifiers that were widely used before its introduction. In this chapter, we present another ensemble of decision trees called Rotation Forest and evaluate its classification performance on different microarray datasets. Rotation Forest can also be applied to different already existing ensembles of classifiers like Random Forest to improve their accuracy and robustness. This study presents evaluation of Rotation Forest classification technique based on decision trees as base classifiers and was evaluated on 14 different datasets with genomic and proteomic data. It is evident that Rotation Forest as well as the proposed rotation of Random Forests outperform most widely used ensembles of classifiers including Random Forests on majority of datasets.

A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data.

BACKGROUND: In the studies of genomics, it is essential to select a small number of genes that are more significant than the others for the association studies of disease susceptibility. In this work, our goal was to compare computational tools with and without feature selection for predicting chronic fatigue syndrome (CFS) using genetic factors such as single nucleotide polymorphisms (SNPs). METHODS: We employed the dataset that was original to the previous study by the CDC Chronic Fatigue Syndrome Research Group. To uncover relationships between CFS and SNPs, we applied three classification algorithms including naive Bayes, the support vector machine algorithm, and the C4.5 decision tree algorithm. Furthermore, we utilized feature selection methods to identify a subset of influential SNPs. One was the hybrid feature selection approach combining the chi-squared and information-gain methods. The other was the wrapper-based feature selection method. RESULTS: The naive Bayes model with the wrapper-based approach performed maximally among predictive models to infer the disease susceptibility dealing with the complex relationship between CFS and SNPs. CONCLUSION: We demonstrated that our approach is a promising method to assess the associations between CFS and SNPs.

[Reviews in comparative genomic research based on orthologs].

The orthologs have similar or even identical functions in different species, share the anological regulatory pathways, and play the close or even same role among species. Furthermore, the vast majority of the biological core functions were assumed to a considerable number of orthologous genes in organisms. Orthologs was the most reliable choices for functional annotation and analysis of genomic sequences, whose unique biological characteristics demonstrated that comparative genomics research based on orthologs will certainly provide clues for detecting the origin, expression, and loss of important functional genes during the biological evolution in different organisms. In this review, the fundamental characteristics of orthologous genes and the relationship between the orthologs and comparison genomics were recounted. The corresponding approaches and the current status in comparative genomic research based on the orthologs were summarized.

Evolution: revisiting the root of the eukaryote tree.

A recent phylogenomic investigation shows that the enigmatic flagellate Breviata is a distinct anaerobic lineage within the eukaryote super-group Amoebozoa and challenges the unikont-bikont rooting of the tree of eukaryotes.

Interpretation of genomic data: questions and answers.

Using a question and answer format we describe important aspects of using genomic technologies in cancer research. The main challenges are not managing the mass of data, but rather the design, analysis, and accurate reporting of studies that result in increased biological knowledge and medical utility. Many analysis issues address the use of expression microarrays but are also applicable to other whole genome assays. Microarray-based clinical investigations have generated both unrealistic hype and excessive skepticism. Genomic technologies are tremendously powerful and will play instrumental roles in elucidating the mechanisms of oncogenesis and in bringing on an era of predictive medicine in which treatments are tailored to individual tumors. Achieving these goals involves challenges in rethinking many paradigms for the conduct of basic and clinical cancer research and for the organization of interdisciplinary collaboration.