EpiDiff: a computational tool for Epigenetic Difference Quantification and Identification by Entropy
   
Tutorials and FAQ about QDMR

   
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QDMR, as the sencond module in EpiDiff, provides a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy. Its platform-free and species-free nature makes it easy for computational biologists to analysis the epigenetic regulation related with DMRs across various temporal and spatial methylomes.

This Tutorial contains the following sections:
Describes how to start Local and online QDMR.
Describes how to preprocess and import methylation data.
Describes how to quantify methylation difference across various samples.
Identify DMRs Describes how to identify DMRs by threshold imbedded in QDMR.
Measure Specificity Describes how to measure sample-specificity for each DMRs.
Export Results Describes how to save results.
Visualization Describes how to display methylation level, DMR distribution and UCSC links.
Getting Started ^Tutorial ^Top
This section describes how to start online and localQDMR.

Before start QDMR, user should start EpiDiff using two ways:
1. Start EpiDiff directly via Java Web Start, using the Java Web Start feature (advantage: no installation required);
2. Download EpiDiff installation package, install and run it locally on your machine (advantage: no network required).

And then, click one the button "Other Services" to change to QDMR service in the following picture.

When first started, QDMR displays the home page.

Import Data ^Tutorial ^Top
There are three ways to load data and start your analysis:

  1) Loading methylation data by clicking the "Import Data" button on the left panel.
  2) Loading methylation data via "File->Import Methylation Data".
  3) Loading methylation data by shortcut keys "Ctrl+I".

QDMR provides the visual interface to import data.

Before import data, please make sure that the data is save in txt file as the format as shown in this example data:

Now Import Methylation Data from Txt or Xls File:

i There are two ways to get your data file:

1.Input or paste the Absolute Path of the data file in the text field of "Input File".
2.Click the "Browser" button to select the data file.

ii Important Notices:
1.It is suggested to refer the example data by click the "example Data 1 or 2" button before import your own data.
2.Information about the regions of interest should be before the methylation data for the region.
3.You can tune the start column of methylation data.
4.Select the Check Box named "Transfer first row as column names" if you want column names as your first row.
5.Column names will be generated automatically if you don't check the box named "Transfer first row as column names".
6.Be sure that methylation value should be in the rage of 0 to max value(1 or 100) according to your methylation data.
7.You must ensure that there are no missing values in your data.
6.The first 20 rows of data will be shown in the data file preview window as any change take places.

After confirmation, click Import button to import data. The following interface will be shown a little while.

Methylation data has been successfully loaded and shown in the data table. The first column named "RegionID" is generated automatically as the ID for each region in QDMR.
Methylation levels in the first row were shown in RegionMethyView acquiescently.
Next you can do each of the following operations:
  1) Click a row to view the methylation level across samples and set the image properties by right click.
  2) Double-click a row to view the region information in the UCSC Genome Browser.
  3) Click "Quantify Difference" button to quantify methylation difference by calculating entropy for all regions.
Quantify Difference ^Tutorial ^Top
Click "Quantify Difference" button to quantify methylation difference by calculating entropy for all regions.
The following interface about quantified methylation difference will be shown when the progress bar reaches 100%.

The methylation difference has been quantified and shown in the entropy table. The first few columns contain the region information. The column named "Entropy" contains the entropy for each region. The last columns are the raw methylation data for each region imported by user.

You can do each of the following operations:
  1) Click a row to view the methylation level across samples and set the image properties by right click.
  2) Double-click a row to view the region information in the UCSC Genome Browser.
  3) Save entropy and raw data via "File->Save Analysis Result->Entropy Table".
  4) Click the "Identify DMRs" button to identify DMRs and N-DMRs for your analysis.
Identify DMRs ^Tutorial ^Top
Click the "Identify DMRs" button to identify DMRs and N-DMRs for your analysis.

The interface for user to set DMR threshold will be provided.


User can Readjust SD to control the methylation difference degree of probability model by which the DMR threshold is determined. Then click OK or Cancel to identify DMRs by DMR threshold. QDMR will identify DMRs from imported regions by the threshold defined by user. The following interface about DMRs will be shown when the progress bar reaches 100%.

DMRs and N-DMRs have been identified and shown in the DMR and N-DMR table, respectively. DMR table contains regions owning entropy less than the DMR threshold. N-DMR table contains regions owning entropy greater than the N-DMR threshold.. Statistics table contains the statistics of regions. And DMR distribution in chromosomes can be shown by clicking the button "DMR Distribution".



Next you can do each of the following operations:
  1) Click a row to view the methylation level across samples and set the image properties by right click.
  2) Double-click a row to view the region information in the UCSC Genome Browser.
  3) Save DMRs and N-DMRs via "File->Save Analysis Result->DMR or N-DMR Table".
  4) See the statistics information and DMR distribution in chromosomes in Statistics Table.
  5) Click the "Measure Specificity" button to measure the sample specificity for all DMRs.
Measure Specificity ^Tutorial ^Top
Click the "Measure Specificity" button to measure the sample specificity for all DMRs. QDMR will calculate the categorical specificity for each region in each sample. The following interface about sample-specificity of each DMR will be shown when the progress bar reaches 100%.

The measurement of sample specificity has been finished and shown in the Specificity Table. The first few columns contain the region information. The column named "Entropy" contains the entropy for each region. The columns named as "CS_" contain the specificity of each region in every sample. The last columns are the raw methylation data for each region imported by user.

Next you can do each of the following operations:
  1) Click a row to view the methylation level across samples and set the image properties by right click.
  2) Double-click a row to view the region information in the UCSC Genome Browser.
  3) Save Specificity Table via "File->Save Analysis Result->Specificity Table".
  4) Save All Results by clicking "Export All Results" or via "File->Save Analysis Result->All Results".
Export Results ^Tutorial ^Top
Save All Results by clicking "Export All Results" or via "File->Save Analysis Result->All Results". The results will be saved in a file containing Entropy Table, DMR Table, N-DMR Table, Specificity Table and Statistics. And then you can analysis the DMRs and N-DMRs in the biological process in which you are interested.

Visualization ^Tutorial ^Top
First, in order to increase the visual effect of methylation data, QDMR provides visualization module RegionMethyView. RegionMethyView shows the methylation levels across various samples and DMR distribution on each chromosome. User can reset and save the figure by right clicking.

Second, in order to show the information near each genome region in user's data, QDMR provides the link to UCSC Genome Browser. User can view the genome features near each region, such as gene, miRNA, SNP, GC percent, CpG island, and histone modifications et al. This view will facilitate the study between DMR and other regulatory elements in the genome.

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1. Public Server/General
  1) Where can I find the hardware and software prerequisites for QDMR?
  A. The hardware requirements, supported operating systems, and supported browsers is shown in Download site.
  2) How can I get help with QDMR or provide feedback?
  A. The tutorial fully describes QDMR and how to use it.
To provide feedback or ask a question please do not hesitate to contact Hongbo Liu (hongbo919@gmail.com) or Yan Zhang (yanyou1225@yahoo.com.cn).

2. Useage

  1) How can I find QDMR in EpiDiff?
  A. QDMR is embedded in EpiDiff as the second module. QDMR service can be found as Tutorial about getting started.
  2) How the threshold of DMR in QDMR is made?
  A.

QDMR is a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy. For more details can refer to a previous paper by us listed following.
Zhang Y, Liu H, Lv J, Xiao X, Zhu J, Liu X, Su J, Li X, Wu Q, Wang F, Cui Y: QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res 2011, 39:e58. [Abstract] [PDF]


3.Data Formats
  1) What file format dose QDMR support?
  A. Currently, QDMR can supports Txt or Xls file. In the latter version, more file formats will be supported.
  2) Where can I find information about file formats used by QDMR?
  A. Information on file formats supported by the modules currently in QDMR is available in Tutorial.

4.Other
If you have any trouble or recommendations, please do not hesitate to contact Hongbo Liu (hongbo919@gmail.com) or Yan Zhang (yanyou1225@yahoo.com.cn).
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