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Using CisGenome to Analyze ChIP‐chip and ChIP‐seq Data
Publication Name:
Current Protocols in Bioinformatics
Unit Number:
Unit 2.13
DOI:
10.1002/0471250953.bi0213s33
Online Posting Date:
March, 2011
Abstract
Chromatin immunoprecipitation (ChIP) coupled with genome tiling array hybridization (ChIP-chip) and ChIP followed by massively parallel sequencing (ChIP-seq) are high-throughput approaches to profiling genome-wide protein-DNA interactions. Both technologies are increasingly used to study transcription-factor binding sites and chromatin modifications. CisGenome is an integrated software system for analyzing ChIP-chip and ChIP-seq data. This unit describes basic functions of CisGenome and how to use them to find genomic regions with protein-DNA interactions, visualize binding signals, associate binding regions with nearby genes, search for novel transcription-factor binding motifs, and map existing DNA sequence motifs to user-supplied genomic regions to define their exact locations.Curr. Protoc. Bioinform. 33:2.13.1-2.13.45. © 2011 by John Wiley & Sons, Inc.
Keywords: transcription factor; chromatin immunoprecipitation; tiling array; next generation sequencing; motif; gene regulation
Table of Contents
- Introduction
- Basic Protocol 1: ChIP-chip Peak Calling for Affymetrix Tiling Array Data
- Basic Protocol 2: Visualization
- Basic Protocol 3: Peak-Gene Association
- Basic Protocol 4: DNA Sequence Retrieval
- Basic Protocol 5: De Novo Motif Discovery
- Basic Protocol 6: Motif Mapping
- Basic Protocol 7: ChIP-chip Peak Calling for Other Tiling Array Platforms
- Basic Protocol 8: ChIP-seq Peak Calling (One-Sample Analysis)
- Basic Protocol 9: ChIP-seq Peak Calling (Two-Sample Analysis)
- Support Protocol 1: Installing CisGenome
- Support Protocol 2: Installing Genome Databases
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
Figures
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Figure 2.13.1 Overview of the CisGenome basic data analysis pipeline. -
Figure 2.13.2 The CisGenome graphic user interface (GUI) and menu system. The menu for creating an Affymetrix tiling array data set is shown as an example. -
Figure 2.13.3 The dialog for adding BPMAP files to an Affymetrix ChIP-chip data set. -
Figure 2.13.4 The dialog for adding CEL files to an Affymetrix ChIP-chip data set. -
Figure 2.13.5 The newly created tiling array data set shown in the CisGenome Project Explorer. Double-clicking a CEL file will open a CisGenome Browser window displaying a heat map of the array image. -
Figure 2.13.6 The dialog for normalizing an Affymetrix tiling array data set. -
Figure 2.13.7 ChIP-chip peak calling. Before peak detection, a normalized tiling array data set (circle 1.10) needs to be available in the Project Explorer, and one needs to provide several basic peak calling parameters in a dialog. -
Figure 2.13.8 ChIP-chip peak calling results. Peaks are summarized in a COD file shown in the right window. A number of BAR files are also created to store enrichment signals. Both the COD file and the BAR files are added to the Project Explorer on the left. -
Figure 2.13.9 CisGenome Browser. (A) The shortcut icon for the browser. (B) The first page of the browser. -
Figure 2.13.10 The browser page for choosing browser session type. -
Figure 2.13.11 An empty browser session newly created. -
Figure 2.13.12 The browser page for choosing data track type. -
Figure 2.13.13 The track configuration page in CisGenome Browser. -
Figure 2.13.14 CisGenome Browser showing different types of data. Tools to adjust the display styles are highlighted. -
Figure 2.13.15 Peak-gene association. (A) The dialog for annotate peaks by nearby genes. (B) The annotation results returned in a COD file. -
Figure 2.13.16 DNA sequence retrieval. (A) The parameter configuration dialog. (B) Returned files. The DNA sequences will be returned in FASTA format (top). If cross-species conservation score is requested, conservation scores for each sequence will be returned as well. The conservation scores can be returned in a text format (bottom left), in BED format (bottom right), or a binary CS format (not shown). -
Figure 2.13.17 The parameter configuration dialog for de novo motif discovery. -
Figure 2.13.18 An example of the summary file produced by de novo motif discovery. -
Figure 2.13.19 Motif matrix files produced by de novo motif discovery. (A) Each motif matrix is stored in a MAT file. (B) The list of motifs is stored in a MATL file. (C) Double-clicking the MATL file in Project Explorer opens CisGenome Browser to display sequence logos of the motifs. The last motif in this example matches the known Gli motif. -
Figure 2.13.20 An example of the CONS file for describing motif consensus sequence. -
Figure 2.13.21 Mapping a motif matrix to a list of genomic regions. (A) The parameter configuration dialog. (B) The mapped motif sites are saved to a COD file. -
Figure 2.13.22 Input data format for calling peaks from ChIP-chip experiments based on non-Affymetrix tiling array platforms. -
Figure 2.13.23 The parameter configuration dialog for normalizing ChIP-chip data from a text file. -
Figure 2.13.24 Converting ChIP-chip data in a text file to a tiling array data set consisting of BAR files. (A) The parameter configuration dialog. (B) The converted data set shown in Project Explorer. -
Figure 2.13.25 A sample ALN file. -
Figure 2.13.26 Loading aligned reads for ChIP-seq peak calling. (A) The parameter configuration dialog for loading the ALN file. (B) Loaded data shown in Project Explorer. -
Figure 2.13.27 FDR computation for an one-sample ChIP-seq experiment. (A) The parameter configuration dialog. (B) The results are returned in a table that summarizes statistical properties of the data. -
Figure 2.13.28 Peak calling from one-sample ChIP-seq data. (A) The parameter configuration dialog. (B) The detected peaks are reported in a COD file. -
Figure 2.13.29 Data for two-sample ChIP-seq analysis loaded into CisGenome. -
Figure 2.13.30 FDR computation for a two-sample ChIP-seq experiment. (A) The parameter configuration dialog. (B) The results are returned in a table that summarizes statistical properties of the data. -
Figure 2.13.31 The parameter configuration dialog for two-sample ChIP-seq peak calling. -
Figure 2.13.32 An example of the CisGenome.ini file. -
Figure 2.13.33 Load a genome database into CisGenome GUI. (A) In the file open dialog, choose the file named [species]_[assembly].cgw in the genome database folder. (B) The loaded database shown in Project Explorer.
Videos
Literature Cited
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