1. www.pazar.info/ PAZAR DATABASE CHIP-SEQ DEPOSIT Wyeth Wasserman

2. Welcome  If you encounter any technical difficulties during the webinar – Type a report using the chat option  Slide presentation ~20 min  Compile Questions as they are submitted and answer them during the final Q&A/discussion period  During the discussion session, we’ll allow audience speaking 2

3. Webinar format  PAZAR introduction  Current status  ChIP-seq data format  Importing procedure  Q&A 3

4. www.pazar.info Software framework for the construction and maintenance of regulatory sequence data annotations Allows multiple boutique databases to function independently within a larger system public repository for regulatory data Each group manages its own deposit and distribution of data Envisioned as tool for capturing deep experimental annotation Species, cell line, treatment 4

5. PAZAR Search Functions 5 TF search: binding sites for a given TF Gene search: regulatory info. for a specific gene Regulatory sequence Pre-computed TF profile

6. More information  Online tutorials  Visit Our 1 st information webinar (2009-11-24) 6 http://www.pazar.info/webinars/webinar2009.html

7. Current Status 7 Registered account: 280 Projects: ~226, including restricted Regulatory seq: 1.17M  Regulating ~80000 genes  Linked to ~1100 TFs Nearly 60 ChIP-Seq projects (data set) now in system

8. ChIP-seq Data Depositing Overview  Create User Account (for first time users)  Create Project  Upload Data  View/Modify Data 8

9. User Account 9 Click “sign in” from the main page

10. User Account 10 For first time user

11. Creating Account 11

12. Creating Project  Project name  1 data set per project  Status – Restricted (only the project-specific users have read and write access) – Published (only the project-specific users have write privileges, but everyone has read access) – Open (everyone has read and write privileges)  Project Description  Project password 12

13. Creating Project 13 Click ‘My Projects’ from the main page

14. ChIP-seq data format  “Called” Peaks  Peak format 1. Chromosome 2. Peak start coordinate 3. Peak end coordinate 4. Max peak height coordinate 5. Score – preferably max peak height if available – assign uniform score if no actual score provided  All coordinates need to be converted to latest genome build  No headers 14

15. Data submission limitations  Max file size: 4MB – Consider splitting larger imports to several files  2 concurrent imports are allowed  We are aware of limitations and are actively pursuing method to increase the uploading speed, thus limit on file size 15

16. Submit Data 16 1. click ‘SUBMIT’ from the main page 2. Select project from pull down menu 3. click ‘chipseq submission’

17. Submit Data 17

18. Email Notification  2 emails – Successful submission – Successful completion of import 18

19. Submission Progress 19 1. click ‘SUBMIT’ from the main page 2. click ‘Check chipseq submissions’ to view the status

20. Submission Progress 20

21. Submit more data to the same project  Due to large file size – Select the same project and repeat the procedure 21

22. View data 22 1. click ‘MY PROJECTS’ from the main page 2. click ‘view data’ for viewing

23. View Data 23 Grouped by gene Grouped by TF

24. View Data: Gene View 24 click to view detail

25. View Data: Detail 25 Max peak coordinate Peak score Gene in proximity

26. Modify Project  Add users to the project  Change project status  Change project description  Deleting project 26

27. Modify Project 27 click ‘MY PROJECTS’ from the main page click ‘edit properties’ to edit

28. Modify Project 28

29. PAZAR future  Continue to improve interface and ease of use and accelerate loading time  Upcoming webinars  Jan 18th 2012 Opposum3: TFBS enrichment analysis  Jan 25th 2012 Pazar: data extraction 29

30. Q&A  Please take a moment to type PAZAR-related questions/comments into the Chat box.  The questions will be answered shortly. 30