ChIP-Array: Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor

Chromatin immunoprecipitation (ChIP) coupled with high-throughput techniques (ChIP-X), such as next generation sequencing (ChIP-Seq) and microarray (ChIP-chip), has been successfully used to map active transcription factor binding sites (TFBS) of a transcription factor (TF). The targeted genes can be activated or suppressed by the TF, or are unresponsive to the TF. Microarray technology has been used to measure the actual expression changes of thousands of genes under the perturbation of a TF, but is unable to determine if the affected genes are direct or indirect targets of the TF. Furthermore, both ChIP-X and microarray methods produce a large number of false positives. Combining microarray expression profiling and ChIP-X data allows more effective TFBS analysis for studying the function of a TF. However, current web servers only provide tools to analyze either ChIP-X or expression data, but not both. Here, we present ChIP-Array, a web server that integrates ChIP-X and expression data from human, mouse, yeast, fruit fly and Arabidopsis. This server will assist biologists to detect direct and indirect target genes regulated by a TF of interest and to aid in the functional characterization of the TF. ChIP-Array is available at http://jjwanglab.hku.hk/ChIP-Array, with free access to academic users. © 2011 The Author(s).published_or_final_versio

Exploring the genome-wide roles of transcription factors and their complexes in chromosome interaction

Session - Bioinformatics and Genomic TechnologyThe tight regulation of genes in different cells is governed by temporal and spatial biological signals. It is very important to pinpoint the pattern of transcription factors (TFs) and their complexes in looping interactions and to detect TF complexes as well as the underlying cis-regulatory modules (CRMs) in different human cell types. Existing studies on analysis of TFs and their complexes were only performed at one dimension and not at genome-wide scale. Recently, the unbiased chromosome conformation capture, Hi-C, can detect the genome-wide chromatin interactions, but has restrictions on its resolution due to the variable cell-to-cell chromosome structures and inadequate sequencing depth. In this study, we provide a comprehensive analysis on TFs regulatory pattern within chromosome looping by combining Hi-C and ENCODE ChIP-Seq data from three human cell types (GM12878, H1-hESC and K562). We first devised a strategy to map ChIP-Seq peaks of each TF to a normalized 10kb Hi-C contact matrix and construct an interaction matrix for each participant TF. We observed tight correlation for TFs participant activities in high resolution chromosome looping between biological replicates, which indicate the TF activities is more stable than local DNA interactions. To check the enrichment of different chromatin marks and genomic features in the interaction region of each participant TF, we performed enrichment test on ...published_or_final_versio

ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks

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ProteoMirExpress: inferring microRNA-centered regulatory networks from high-throughput proteomic and transcriptome data

MicroRNAs (miRNAs) regulate gene expression through translational repression and RNA degradation. Recently developed high-throughput proteomic methods measure gene expression changes at protein levels, and therefore can reveal the direct effects of miRNAs’ translational repression. Here, we present a web server, ProteoMirExpress that integrates proteomic and mRNA expression data together to infer miRNA-centered regulatory networks. With both high throughput data from the users, ProteoMirExpress is able to discover not only miRNA targets that have mRNA decreased, but also subgroups of targets whose proteins are suppressed but mRNAs are not significantly changed or whose mRNAs are decreased but proteins are not significantly changed, which were usually ignored by most current methods. Furthermore, both direct and indirect targets of miRNAs can be detected. Therefore ProteoMirExpress provides more comprehensive miRNA-centered regulatory networks. We use several published data to assess the quality of our inferred networks and prove the value of our server. ProteoMirExpress is available at http://jjwanglab.org/ProteoMirExpress, with free access to academic users.postprin

Application of Deep Learning Long Short-Term Memory in Energy Demand Forecasting

The smart metering infrastructure has changed how electricity is measured in both residential and industrial application. The large amount of data collected by smart meter per day provides a huge potential for analytics to support the operation of a smart grid, an example of which is energy demand forecasting. Short term energy forecasting can be used by utilities to assess if any forecasted peak energy demand would have an adverse effect on the power system transmission and distribution infrastructure. It can also help in load scheduling and demand side management. Many techniques have been proposed to forecast time series including Support Vector Machine, Artificial Neural Network and Deep Learning. In this work we use Long Short Term Memory architecture to forecast 3-day ahead energy demand across each month in the year. The results show that 3-day ahead demand can be accurately forecasted with a Mean Absolute Percentage Error of 3.15%. In addition to that, the paper proposes way to quantify the time as a feature to be used in the training phase which is shown to affect the network performance

Eliminación de DBP en aceite de onagra mediante arcilla activada modificada por chitosán y CTAB

The pollution of phthalic acid esters (PAEs) in edible oils is a serious problem. In the current study, we attempt to remove dibutyl phthalate ester (DBP) from evening primrose oil (EPO) with modified activated clay. The activated clay, commonly used for de-coloration in the oil refining process, was modified by chitosan and hexadecyl trimethyl ammonium bromide (CTAB). The modifications were characterized by SEM, XRD, and FT-IR. We further tested the DBP adsorption capacity of CTAB/chitosan-clay and found that the removal rate was 27.56% which was 3.24 times higher than with pristine activated clay. In addition, the CTAB/chitosan-clay composite treatment had no significant effect on the quality of evening primrose oil. In summary, the CTAB/chitosan-clay composite has a stronger DBP adsorption capacity and can be used as a new adsorbent for removing DBP during the de-coloration process of evening primrose oil.La contaminación por ésteres de ácido ftálico (PAEs) en los aceites comestibles es un problema grave. En el presente estudio, intentamos eliminar el éster de ftalato de dibutilo (DBP) del aceite de onagra (EPO) con arcilla activada modificada. La arcilla activada, comúnmente utilizada en la decoloración en el proceso de refinación de los aceites, fue modificada con chitosán y bromuro de hexadecil trimetil amonio (CTAB). Las modificaciones se caracterizaron mediante SEM, XRD y FT-IR. Además, probamos la capacidad de adsorción de DBP de CTAB / chitosán-arcilla y descubrimos que la tasa de eliminación era del 27,56%, que era 3,24 veces mayor que la arcilla activada pura. Además, el tratamiento compuesto de CTAB/chitosán-arcilla no tuvo un efecto significativo sobre la calidad del aceite de onagra. En resumen, el compuesto CTAB/chitosán-arcilla tiene una capacidad de adsorción de DBP más fuerte y se puede utilizar como un nuevo adsorbente para eliminar DBP durante el proceso de decoloración del aceite de onagra

Plasmodium falciparum (Haemosporodia: Plasmodiidae) and O'nyong-nyong virus development in a transgenic Anopheles gambiae (Diptera: Culicidae) strain

Transgenic Anopheles gambiae Giles (Diptera: Culicidae) mosquitoes have been developed that confer sexual sterility on males that carry a transgene encoding a protein which cuts ribosomal DNA. A relevant risk concern with transgenic mosquitoes is that their capacity to transmit known pathogens could be greater than the unmodified form. In this study, the ability to develop two human pathogens in these transgenic mosquitoes carrying a homing endonuclease which is expressed in the testes was compared with its nontransgenic siblings. Infections were performed with Plasmodium falciparum (Welch) and o'nyong-nyong virus (ONNV) and the results between the transgenic and nontransgenic sibling females were compared. There was no difference observed with ONNV isolate SG650 in intrathoracic infections or the 50% oral infectious dose measured at 14 d postinfection or in mean body titers. Some significant differences were observed for leg titers at the medium and highest doses for those individuals in which virus titer could be detected. No consistent difference was observed between the transgenic and nontransgenic comparator females in their ability to develop P. falciparum NF54 strain parasites. This particular transgene caused no significant effect in the ability of mosquitoes to become infected by these two pathogens in this genetic background. These results are discussed in the context of risk to human health if these transgenic individuals were present in the environment

EpiRegNet: constructing epigenetic regulatory networks from high throughput gene expression data for humans

Poster Presentation: P-H010SUMMARY: EpiRegNet, an interactive web server, is able to construct an epigenetic regulatory network (ERN) from gene expression data, including microarray and RNA-seq data for human ESC, IMR90 and CD4+ T cells. Given a set of categorized genes, the system will find the epigenetic factors that contribute most to the differences in the gene expression and construct an ERN around these factors. Furthermore, the web server can demonstrate cooperative/competitive relationships among these factors in activating or repressing their target genes. Availability and Implementation: EpiRegNet is freely available on the web at http://wanglab.hku.hk/EpiRegNet/. It is implemented in perl, PHP and MySQL with all major browsers supported.postprintThe 2011 Hong Kong Inter-University Biochemistry Postgraduate Symposium, Hong Kong, 11 June 2011

Genes Underlying Positive Influence Of Prenatal Environmental Enrichment And Negative Influence Of Prenatal Earthquake Simulation And Corrective Influence Of Chinese Herbalmedicine On Rat Offspring: Irf7 And Ninj2

Background: Prenatal environmental enrichment (EE) has been proven to positively affect but prenatal stress negatively influence the physiological and psychological processes in animals, whose trans-generational genetic mechanism remains unclearly defined. We aimed to investigate and find out key genes underlying the positive-negative effects derived from prenatal interventions.Materials and Methods: Pregnant rats were randomized into EE group (EEG), earthquake simulation group (ESG), herbal group (HG) received herbal supplements in feed after earthquake simulation, and control group (CG).Results: Light Box Defecation Test (LBDT) showed EEG offspring presented less fecal pellets than CG offspring, ESG’s more than CG’s, and HG’s less than ESG (p’s<0.05). Open-field Test (OFT) score of EEG was higher than CG offspring, of ESG’s was lower than CG’s, and HG’s higher than ESG’s. Irf7 and Ninj were screened, which were up-regulated in EEG, down-regulated in ESG (FC<0.5), and were neutralized in HG. Prenatal EE could positively promote the nervous system development, prenatal earthquake simulation could retard the nervous system development and Chinese herbal remedy (JKSQW) which could correct the retardation.Conclusion: The negative-positive prenatal effect could contribute to altered gene expression of Irf7 and Ninj2 which also could play a key role in the improving function of JKSQWfor the kidneys.Keywords: Prenatal stress; Earthquake simulation; Light Box Defecation Test; Open-field Test; Irf7; Ninj