visualization tool for microarray data stored in chado

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visualization tool for microarray data stored in chado

Peili Zhang
Hello!

Can anyone recommend software tools for the visualization and simple querying of microarray data stored in chado-like relational database? I only need the very basic functionality, such as looking up a gene or a list of genes in certain samples and viewing the histograms or line graphs of the expression levels across samples. I don't need to have statistical analysis capability embedded in the tool but wouldn't mind having it available. The best scenario would be that there're libraries/modules visualizing microarray data in chado for plug and play. 

Thanks very much for any information you can share!

Best Regards,

Peili Zhang, Ph.D.

Senior Research Scientist

Computational Sciences

Vertex Pharmaceuticals, Inc.

50 Northern Avenue

Bsoton, MA 02210

Tel: 617-341-6593

www.vrtx.com

 

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Re: visualization tool for microarray data stored in chado

Scott Cain
HI Peili,

The only group I know of that used Chado for microarray data is Stan Nelson's group at UCLA.  Brian O'Connor and Allen Day are alumni of that group, so they might be able to help, but that was quite some time ago.  Also, I'm going to cc this to the schema mailing list, which is where Chado-related stuff gets discussed.

Scott



On Fri, Feb 7, 2014 at 7:36 AM, Peili Zhang <[hidden email]> wrote:
Hello!

Can anyone recommend software tools for the visualization and simple querying of microarray data stored in chado-like relational database? I only need the very basic functionality, such as looking up a gene or a list of genes in certain samples and viewing the histograms or line graphs of the expression levels across samples. I don't need to have statistical analysis capability embedded in the tool but wouldn't mind having it available. The best scenario would be that there're libraries/modules visualizing microarray data in chado for plug and play. 

Thanks very much for any information you can share!

Best Regards,

Peili Zhang, Ph.D.

Senior Research Scientist

Computational Sciences

Vertex Pharmaceuticals, Inc.

50 Northern Avenue

Bsoton, MA 02210

Tel: <a href="tel:617-341-6593" value="+16173416593" target="_blank">617-341-6593

www.vrtx.com

 

This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: visualization tool for microarray data stored in chado

Peili Zhang
Thanks, Scott! It's been a long time. Hope all is well.


Peili Zhang, Ph.D.

Senior Research Scientist

Computational Sciences

Vertex Pharmaceuticals, Inc.

50 Northern Avenue

Bsoton, MA 02210

Tel: 617-341-6593

www.vrtx.com

 


From: Scott Cain <[hidden email]>
Date: Friday, February 7, 2014 3:08 PM
To: Peili Zhang <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, GMOD Schema/Chado List <[hidden email]>, Brian O'Connor <[hidden email]>, Allen Day <[hidden email]>
Subject: Re: [GMOD-devel] visualization tool for microarray data stored in chado

HI Peili,

The only group I know of that used Chado for microarray data is Stan Nelson's group at UCLA.  Brian O'Connor and Allen Day are alumni of that group, so they might be able to help, but that was quite some time ago.  Also, I'm going to cc this to the schema mailing list, which is where Chado-related stuff gets discussed.

Scott



On Fri, Feb 7, 2014 at 7:36 AM, Peili Zhang <[hidden email]> wrote:
Hello!

Can anyone recommend software tools for the visualization and simple querying of microarray data stored in chado-like relational database? I only need the very basic functionality, such as looking up a gene or a list of genes in certain samples and viewing the histograms or line graphs of the expression levels across samples. I don't need to have statistical analysis capability embedded in the tool but wouldn't mind having it available. The best scenario would be that there're libraries/modules visualizing microarray data in chado for plug and play. 

Thanks very much for any information you can share!

Best Regards,

Peili Zhang, Ph.D.

Senior Research Scientist

Computational Sciences

Vertex Pharmaceuticals, Inc.

50 Northern Avenue

Bsoton, MA 02210

Tel: <a href="tel:617-341-6593" value="&#43;16173416593" target="_blank"> 617-341-6593

www.vrtx.com

 

This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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Read the Whitepaper.
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------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.
------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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