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www.pazar.info/ PAZAR DATABASE CHIP-SEQ DEPOSIT Wyeth Wasserman
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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
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Webinar format PAZAR introduction Current status ChIP-seq data format Importing procedure Q&A 3
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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
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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
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More information Online tutorials Visit Our 1 st information webinar (2009-11-24) 6 http://www.pazar.info/webinars/webinar2009.html
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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
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ChIP-seq Data Depositing Overview Create User Account (for first time users) Create Project Upload Data View/Modify Data 8
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User Account 9 Click “sign in” from the main page
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User Account 10 For first time user
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Creating Account 11
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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
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Creating Project 13 Click ‘My Projects’ from the main page
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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
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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
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Submit Data 16 1. click ‘SUBMIT’ from the main page 2. Select project from pull down menu 3. click ‘chipseq submission’
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Submit Data 17
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Email Notification 2 emails – Successful submission – Successful completion of import 18
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Submission Progress 19 1. click ‘SUBMIT’ from the main page 2. click ‘Check chipseq submissions’ to view the status
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Submission Progress 20
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Submit more data to the same project Due to large file size – Select the same project and repeat the procedure 21
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View data 22 1. click ‘MY PROJECTS’ from the main page 2. click ‘view data’ for viewing
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View Data 23 Grouped by gene Grouped by TF
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View Data: Gene View 24 click to view detail
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View Data: Detail 25 Max peak coordinate Peak score Gene in proximity
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Modify Project Add users to the project Change project status Change project description Deleting project 26
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Modify Project 27 click ‘MY PROJECTS’ from the main page click ‘edit properties’ to edit
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Modify Project 28
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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
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Q&A Please take a moment to type PAZAR-related questions/comments into the Chat box. The questions will be answered shortly. 30
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