# Creating a list of enriched regions

In this section, we will create a list of peaks significantly enriched in the ChIP sample versus the control sample.

* Select **Create a list of enriched regions** from the *Peak Analysis* section of the *ChIP-Seq* workflow
* Select **Specify New Criteria** (Figure 1)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-4dc321f6319eb04baef8bf38051207bac1d0ffde%2F2017-07-26%2012_30_42-List%20Creator.png?alt=media)

Figure 1. List creator for ChIP-Seq data allows you to create lists using preset or custom criteria

Configure the new criteria as shown (Figure 2).

* Name the criteria **p-value filtered**
* Select **1/regions (peaks)** from the *Spreadsheet* drop-down menu
* Select **11. p-value(Sample ID vs. mock)** from the *Column* drop-down menu
* Select **significant with FDR of** from the *include p-values* drop-down menu with a value of **0.05**

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-f6f1f38da6909056efdb053ec1c3bb907efffcc8%2F2017-07-26%2012_31_13-Configure%20Criteria.png?alt=media)

Figure 2. Creating a criteria that includes regions significantly enriched in ChIP vs. mock

* Select **OK** to add the criteria to the criteria list (Figure 3)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-d66eb4425f5b44719857e8d597ddeb3b6217c45e%2F2017-07-26%2012_31_31-List%20Creator.png?alt=media)

Figure 3. New criteria are added to the criteria list

* Select **Save**
* Select **p-value filtered** from the list of criteria (Figure 4)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-a905fcbeb41aa81cb884e47235661479a4052d34%2F2017-07-26%2012_31_39-List%20Creator.png?alt=media)

Figure 4. Choosing criteria to save as lists

* Select **OK**

The new spreadsheet will open (Figure 5).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c1e1e23f2de7ba7266a49fa0a94478397f9ea105%2F2017-08-09%2014_16_22-Partek%20Genomics%20Suite%20-%201_p-value_filtered%20\(p-value%20filtered.txt\).png?alt=media)

Figure 5. Spreadsheet with regions that are significantly enriched in the ChIP sample vs. control

Other *List Creator* operations like the *Venn Diagram,* *Union (Or),* and *Intersection (And)* of the lists could be used to create different lists of enriched peaks. For example, you could filter on the intersection between *Strand Separation FDR of 0.05* and *Peaks not in mock* or filter by *scaled fold change* or apply a minimum number of reads per million. The choice of what peaks you want to consider for downstream analysis depends on the goals and details of your experimental design.

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.