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No thanks Submit review. Figure 2. Picking out the native conformation using physics-based atomically detailed models, sampled by molecular dynamics, is presently beyond the reach of computer methods. It gives each gene an expression behavior but ignores the distance between binding sites, and it considers all genes kb within the binding peaks as potential targets. The ground mesostrings are classified in terms of either a reverse-turn or a helical-turn conformation see Figure 1. The beta version is constantly upgraded with new features, some of which are then removed. View full description.

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For data input, basic commands indicate the following parameters additional, optional BETA parameters can be found in Box 2: BETA analysis of example data sets. TF activating and repressive function prediction and direct target detection. The screen output lists all arguments used in this procedure, reports the input file format checking status and shows warnings and progress.

In the end, BETA also reports the total time of the procedure. An example of this screen information is shown:. Predict Tet1 function and direct targets in mouse ES cells. Input Tet1 BED format peak file via -p and input the differential expression file via -e; set the genome assembly mm9 via -g:.

TF activating and repressive function prediction, direct target detection and motif analysis. This parameter can be specified depending on the data set. This boundary file allows other data with at least three-column BED format, and it can be set via the parameters in Box 3. Troubleshooting advice can be found in Table 2. The run time is closely related to the number of binding events users can set top binding sites by using the parameter --pn and the number the differentially expressed genes which depends on —da and --df.

The resulting output files are listed here:. Functional prediction results are presented as a cumulative distribution function plot; direct target genes can be downloaded as a tab-delimited text file with the first six columns in standard BED format.

All the output results have the same format with the AR output shown in the Experimental design. The dashed line indicates the non-differentially-expressed NON genes as background. BETA-plus runs function prediction, target detection and binding motif analysis step by step. If a factor functions as both an activator and a repressor of gene expression e. The binding motif analysis file betamotif.

The result of the ESR1 analysis are shown in Figure 4 , with Figure 4a,b depicting binding motifs found in upregulated and downregulated target gene regions, respectively.


The ESR1 binding motif was the most significant one in both up- and down-target regions. Motifs with a positive t score represent enrichment in upregulated genes Fig. In addition, binding motifs found in upregulated and downregulated genes compared with nontargeted genes represent potential collaborating factors to ESR1 Fig. ESR1, ESR2 and six other human estrogen receptor family members are classified into one group because of their high similarity scores.

In addition to. Additional files display the results of motif comparisons: PSSM an example is shown below can be used to draw a motif logo, to perform motif similarity comparisons or to get the motif sequence for further analysis; t scores and P values represent the statistical values for the enrichment.

BETA-minus predicts factor target genes from binding data only, and provides as output two text files: The target-associated peaks file has the same format as BETA-basic output files. A sample output for the target gene file is shown below, where score refers to the regulatory potential calculated with the same method we described above:. The three subprotocols provided by the BETA package have a wide applicability for the integration of ChIP-seq and transcriptome analysis.

Target genes predicted by BETA and the prediction of their activating or repressing functions help researchers to understand the regulatory mechanisms of the analyzed factors. Furthermore, efficient binding motif analysis provides a new way to detect co-regulators. All authors contributed to the discussion and writing of the final manuscript. Reprints and permissions information is available online at http: National Center for Biotechnology Information , U.

Target analysis by integration of transcriptome and ChIP-seq data with BETA

Nat Protoc. Author manuscript; available in PMC Aug Author information Copyright and License information Disclaimer. Correspondence should be addressed to Y.

Copyright notice. The publisher's final edited version of this article is available at Nat Protoc. See other articles in PMC that cite the published article. Abstract The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression. Development of the protocol We developed BETA as an integrated software package for analyzing factor binding and differential expression in mammalian genomes.

Open in a separate window. Figure 1. Comparison with other methods Various methods and software process ChIP-seq data and analyze TF target genes with different strategies. Experimental design To illustrate how this protocol works and to interpret its results, we use androgen receptor AR ChIP-chip data obtained in LNCaP cells in combination with microarray data of gene expression after 16 h of dihydrotestosterone DHT treatment.

Value adj. Figure 2.

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Direct target prediction BETA predicts factor target genes by combining the binding potential from ChIP-seq data with differential expression data.

This is an example of the top lines of that output for direct target gene prediction: Here we show the associated peaks of AR-upregulated target genes as follows: Binding motif analysis To identify factor-binding motifs associated with ChIP-seq and differential expression data, BETA conducts motif analysis on sites proximal to the targets. Box 1 Differential expression data file formats. Application of BETA beyond human and mouse data: Binding file name Binding data resource Data description Peak no.

Expression file name Expression data accession no. Step Problem Possible reason Solution 1—6 Installation failed Variable problems and see below Refer to the readme or detailed installation online http: The resulting output files are listed here: Figure 3.

Figure 4.

Target analysis by integration of transcriptome and ChIP-seq data with BETA

A sample output for the target gene file is shown below, where score refers to the regulatory potential calculated with the same method we described above: Argument List: References 1. McLean CY, et al. GREAT improves functional interpretation of cis -regulatory regions.

Nat Biotechnol. Nucleic Acids Res. A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nat Genet.

Palii CG, et al.

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages. EMBO J. Tang Q, et al. A comprehensive view of nuclear receptor cancer cistromes. Cancer Res. Rank products: FEBS Lett. Sherman BT, et al. Ma W, Wong WH. The analysis of ChIP-seq data. Methods Enzymol. Zang C, et al. A clustering approach for identification of enriched domains from histone modification ChIP-seq data.

Boyer LA, et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Rougemont J, Naef F.


Methods Mol Biol. Prediction of regulatory networks: Honkela A, et al.

Model-based method for transcription factor target identification with limited data. Proc Natl Acad Sci. Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana.