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

Overexpression of ubiquitin specific peptidase 14 predicts unfavorable prognosis in esophageal squamous cell carcinoma

published_or_final_versio

Broadband spin-controlled focusing via logarithmic-spiral nanoslits of varying width

This work presents analytical, numerical and experimental demonstrations of light diffracted through a logarithmic spiral (LS) nanoslit, which forms a type of switchable and focus-tunable structure. Owing to a strong dependence on the incident photon spin, the proposed LS-nanoslit converges incoming light of opposite handedness (to that of the LS-nanoslit) into a confined subwavelength spot, while it shapes light with similar chirality into a donut-like intensity profile. Benefitting from the varying width of the LS-nanoslit, different incident wavelengths interfere constructively at different positions, i.e., the focal length shifts from 7.5 μm (at λ = 632.8 nm) to 10 μm (at λ = 488 nm), which opens up new opportunities for tuning and spatially separating broadband light at the micrometer scale

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

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

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

published_or_final_versio

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

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