Widget Request

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Widget Request

Vallejos, Andrew

Would it be possible to make a hybrid Ontology Enrichment Widget and Expression Widget? The goal would be to create an expression widget that uses tissues selected for their enrichment, rather than using a pre-slimed list on anatomical terms.

 

Thanks,

 

Andrew

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]


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Re: Widget Request

Richard Smith
Do you mean:
1) perform an enrichment analysis in tissue expression to find
significant tissues for the list
2) show an expression graph for only these tissues?  (with number
of genes from the list expressed in the tissue)

If so, it might make sense to have a toggle on the widget to switch
between 'show all' and 'show enriched'

Richard.




On 20/07/2011 19:35, Vallejos, Andrew wrote:

> Would it be possible to make a hybrid Ontology Enrichment Widget and
> Expression Widget? The goal would be to create an expression widget that
> uses tissues selected for their enrichment, rather than using a
> pre-slimed list on anatomical terms.
>
>
>
> Thanks,
>
>
>
> Andrew
>
>
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: Widget Request

Vallejos, Andrew
My concern with show all would be length.  Also would you still show
parental terms in a show all list or only the tissue terms with direct
annotation?

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Richard Smith
Sent: Monday, July 25, 2011 4:34 AM
To: [hidden email]
Subject: Re: [InterMine Dev] Widget Request

Do you mean:
1) perform an enrichment analysis in tissue expression to find
significant tissues for the list
2) show an expression graph for only these tissues?  (with number
of genes from the list expressed in the tissue)

If so, it might make sense to have a toggle on the widget to switch
between 'show all' and 'show enriched'

Richard.




On 20/07/2011 19:35, Vallejos, Andrew wrote:
> Would it be possible to make a hybrid Ontology Enrichment Widget and
> Expression Widget? The goal would be to create an expression widget
that

> uses tissues selected for their enrichment, rather than using a
> pre-slimed list on anatomical terms.
>
>
>
> Thanks,
>
>
>
> Andrew
>
>
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: Widget Request

Richard Smith
> My concern with show all would be length.  Also would you still show
> parental terms in a show all list or only the tissue terms with direct
> annotation?

What source of expression data are you thinking about for this?

Richard.



> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On
> Behalf Of Richard Smith
> Sent: Monday, July 25, 2011 4:34 AM
> To: [hidden email]
> Subject: Re: [InterMine Dev] Widget Request
>
> Do you mean:
> 1) perform an enrichment analysis in tissue expression to find
> significant tissues for the list
> 2) show an expression graph for only these tissues?  (with number
> of genes from the list expressed in the tissue)
>
> If so, it might make sense to have a toggle on the widget to switch
> between 'show all' and 'show enriched'
>
> Richard.
>
>
>
>
> On 20/07/2011 19:35, Vallejos, Andrew wrote:
>> Would it be possible to make a hybrid Ontology Enrichment Widget and
>> Expression Widget? The goal would be to create an expression widget
> that
>> uses tissues selected for their enrichment, rather than using a
>> pre-slimed list on anatomical terms.
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Andrew
>>
>>
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>


_______________________________________________
dev mailing list
[hidden email]
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Re: Widget Request

Vallejos, Andrew
The expression data would come from GEO.  The data that is being loaded
into RatMine is simple in that it uses the AffyMetrix call of Present or
Absent for a given probeset.  The probeset is then mapped to a gene,
inferring the presence or absence of a gene in a tissue for a given
experimental condition.  But basically we would be displaying a count of
the present / absent calls.

-Andrew

-----Original Message-----
From: www-data [mailto:[hidden email]] On Behalf Of Richard Smith
Sent: Monday, July 25, 2011 10:04 AM
To: Vallejos, Andrew
Cc: Richard Smith; [hidden email]
Subject: RE: [InterMine Dev] Widget Request

> My concern with show all would be length.  Also would you still show
> parental terms in a show all list or only the tissue terms with direct
> annotation?

What source of expression data are you thinking about for this?

Richard.



> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On
> Behalf Of Richard Smith
> Sent: Monday, July 25, 2011 4:34 AM
> To: [hidden email]
> Subject: Re: [InterMine Dev] Widget Request
>
> Do you mean:
> 1) perform an enrichment analysis in tissue expression to find
> significant tissues for the list
> 2) show an expression graph for only these tissues?  (with number
> of genes from the list expressed in the tissue)
>
> If so, it might make sense to have a toggle on the widget to switch
> between 'show all' and 'show enriched'
>
> Richard.
>
>
>
>
> On 20/07/2011 19:35, Vallejos, Andrew wrote:
>> Would it be possible to make a hybrid Ontology Enrichment Widget and
>> Expression Widget? The goal would be to create an expression widget
> that
>> uses tissues selected for their enrichment, rather than using a
>> pre-slimed list on anatomical terms.
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Andrew
>>
>>
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev