www.pazar.info/

PAZAR DATABASE CHIP-SEQ DEPOSIT

Wyeth Wasserman

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

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Webinar format

PAZAR introduction

Current status

ChIP-seq data format

Importing procedure

Q&A

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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

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PAZAR Search Functions

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TF search: binding sites for a given TFGene search: regulatory info. for a specific geneRegulatory sequencePre-computed TF profile

More information

Online tutorials

Visit Our 1st information webinar (2009-11-24)

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http://www.pazar.info/webinars/webinar2009.html

Current Status

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• 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

ChIP-seq Data Depositing Overview

Create User Account (for first time users)

Create Project

Upload Data

View/Modify Data

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User Account

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Click “sign in” from the main page

User Account

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For first time user

Creating Account

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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

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Creating Project

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Click ‘My Projects’ from the main page

ChIP-seq data format

“Called” Peaks Peak format

1. Chromosome2. Peak start coordinate3. Peak end coordinate4. Max peak height coordinate5. 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

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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

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Submit Data

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1. click ‘SUBMIT’ from the main page

2. Select project from pull down menu

3. click ‘chipseq submission’

Submit Data

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Email Notification

2 emails– Successful submission– Successful completion of import

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Submission Progress

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1. click ‘SUBMIT’ from the main page

2. click ‘Check chipseq submissions’ to view the status

Submission Progress

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Submit more data to the same project

Due to large file size

– Select the same project and repeat the procedure

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View data

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1. click ‘MY PROJECTS’ from the main page

2. click ‘view data’ for viewing

View Data

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Grouped by gene

Grouped by TF

View Data: Gene View

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click to view detail

View Data: Detail

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Max peak coordinate

Peak score

Gene in proximity

Modify Project

Add users to the project

Change project status

Change project description

Deleting project

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Modify Project

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click ‘MY PROJECTS’ from the main page

click ‘edit properties’ to edit

Modify Project

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PAZAR future

Continue to improve interface and ease of use and accelerate loading time

Upcoming webinars

Jan 18th 2012Opposum3: TFBS enrichment analysis

Jan 25th 2012Pazar: data extraction

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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.

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