Análisis estadístico de los espectros de frecuencia de las regiones reguladoras del ENCODE / Statistical analysis of the Fourier Spectra of the ENCODE regulatory regions

RESUMEN En la actualidad, nuevas bases de datos genómicos (secuencias de ADN) son puestas al alcance del dominio público para su análisis. La bioinformática ha desarrollado algoritmos para extraer información y características de dichas secuencias. Sin embargo, estos algoritmos bioinformáticos tienen limitaciones. Una alternativa es utilizar herramientas propias del procesamiento digital de señales (DSP) adaptadas a secuencias genómicas (procesamiento de señales genómicas - GSP). El presente trabajo versa sobre el análisis de los cuatro primeros momentos centrales (media, desviación estándar, asimetría y curtosis) y dos momentos estadísticos (mediana y varianza) de los espectros frecuenciales de las 15 Regiones Reguladoras (RRs) de la base de datos ENCODE con el objetivo de estudiar diferencias estadísticas y frecuencias características. La base de datos seleccionada es "mapeada". Luego, la FFT es calculada a estas señales genómicas y finalmente los momentos estadísticos son implementados. Los resultados mues tran la existencia de 3 grupos de RRs utilizando la media, mediana y curtosis. La desviación estándar y la varianza, parecen no resaltar información importante. Finalmente, la asimetría revela un comportamiento homogéneo ante la presencia de valores atípicos en algunas RRs. Estas observaciones permiten inferir que la periodicidad dentro de la secuencia está relacionada o podría determinar la función biológica que desempeña la misma secuencia.

ABSTRACT Nowadays, new genomic databases (DNA sequences) are available to the whole scientist community for its analysis. The bioinformatics has developed algorithms to extract information and features of the sequences. However, the bioinformatics algorithms have restrictions. An alternative is the use of digital signal processing (DSP) tools adapted to genomic sequences (genomic signal processing - GSP). This work analyzes the first four statistics moments (mean, standard deviation, skewness and kurtosis) and other two moments (median and variance) of the frequency spectra of 15 regulatory regions (RRs) in ENCODE database with the main objective of studying the statistics di fferences and frequency features. The selected database is mapped. Then, the FFT is calculated to these genomic signals and finally the statistic moments implemented. The results show a three-group behavior in the RRs with the mean, median and kurtosis. The deviations standard and the variance do not show important behavior. Finally, the skewness shows a homogeneous behavior with the lack of atypical values in some RRs. These observations support the idea of the presence of periodicities in a sequence that may be related or may determine the biological function that a sequence may perform.

Human Transcriptome and Chromatin Modifications: An ENCODE Perspective

A decade-long project, led by several international research groups, called the Encyclopedia of DNA Elements (ENCODE), recently released an unprecedented amount of data. The ambitious project covers transcriptome, cistrome, epigenome, and interactome data from more than 1,600 sets of experiments in human. To make use of this valuable resource, it is important to understand the information it represents and the techniques that were used to generate these data. In this review, we introduce the data that ENCODE generated, summarize the observations from the data analysis, and revisit a computational approach that ENCODE used to predict gene expression, with a focus on the human transcriptome and its association with chromatin modifications.

ENCODE: A Sourcebook of Epigenomes and Chromatin Language

Until recently, since the Human Genome Project, the general view has been that the majority of the human genome is composed of junk DNA and has little or no selective advantage to the organism. Now we know that this conclusion is an oversimplification. In April 2003, the National Human Genome Research Institute (NHGRI) launched an international research consortium called Encyclopedia of DNA Elements (ENCODE) to uncover non-coding functional elements in the human genome. The result of this project has identified a set of new DNA regulatory elements, based on novel relationships among chromatin accessibility, histone modifications, nucleosome positioning, DNA methylation, transcription, and the occupancy of sequence-specific factors. The project gives us new insights into the organization and regulation of the human genome and epigenome. Here, we sought to summarize particular aspects of the ENCODE project and highlight the features and data that have recently been released. At the end of this review, we have summarized a case study we conducted using the ENCODE epigenome data.

Application of Multi-stage Classification and Encoding in Medical Consumable Materials / 医疗卫生装备

The basic principles and methods of information classification and encoding, as well as the present situation of classification of medical consumable materials, are introduced. By adopting multi-stage classification and encoding structure to information of medical consumable materials, the classification and encoding become more scientific, flexible and practical, which avails the informational management of medical consumable materials.

The Advance in Research of Banana Bunchy Top Virus / 微生物学通报

Banana bunchy top virus (BBTV) is the pathogen of banana bunchy top disease (BBTD); it seriously disserves the banana production. This paper reviewed the separation and purification methods, classifying and taxonomy status of BBTV; the genome structure and function of each encode protein of the virus; and the present problems that should be further clarified.