[BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

[BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

Estrella, Heather
ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

Hi,

In looking at the mutation frequencies reported for the Pancreatic Cancer (JHU/US) dataset, it reports the frequencies out of n=114. Can you please send me the reference to the source data behind whats reported for Pancreatic Cancer (JHU/US)?

Thanks,

Heather


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

Elena Rivkin
Heather, 
These data were derived from the following publication:

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses


Siân Jones1,* et al


Science. 2008 September 26; 321(5897): 1801–1806. doi:10.1126/science.1164368.


Elena




From: "Estrella, Heather" <[hidden email]>
Date: Mon, 21 Mar 2011 12:08:21 -0400
To: "[hidden email]" <[hidden email]>
Subject: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

Hi,

In looking at the mutation frequencies reported for the Pancreatic Cancer (JHU/US) dataset, it reports the frequencies out of n=114. Can you please send me the reference to the source data behind whats reported for Pancreatic Cancer (JHU/US)?

Thanks,

Heather


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

Estrella, Heather

Thanks Elena,

 

That’s the reference I was thinking the data was probably from. The total number of samples used for genetic analysis in this study was 24 not 114. Can you please look into correcting the summary stats so that the correct frequency is reported for mutations?

 

In looking at the sample names for this study in BioMart, it looks like additional studies were added to the BioMart dataset. Maybe that’s where the n-114 came from. However, that messes up the frequencies as not all the genes were tested in all 114 samples.

 

Many thanks,

Heather

 

From: Elena Rivkin [mailto:[hidden email]]
Sent: Monday, March 21, 2011 9:14 AM
To: Estrella, Heather; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Heather, 

These data were derived from the following publication:

 

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

 

Siân Jones1,* et al

 

Science. 2008 September 26; 321(5897): 1801–1806. doi:10.1126/science.1164368.

 

Elena

 

 

 

From: "Estrella, Heather" <[hidden email]>
Date: Mon, 21 Mar 2011 12:08:21 -0400
To: "[hidden email]" <[hidden email]>
Subject: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Hi,

In looking at the mutation frequencies reported for the Pancreatic Cancer (JHU/US) dataset, it reports the frequencies out of n=114. Can you please send me the reference to the source data behind what’s reported for “Pancreatic Cancer (JHU/US)”?

Thanks,

Heather


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

Jianxin Wang

Heather,

 

 

Yes, the 114 samples are from their “discovery” studies (24 samples) and “prevalence” studies (the rest of them).

 

Jason

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Estrella, Heather
Sent: Monday, March 21, 2011 11:38 AM
To: Elena Rivkin; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Thanks Elena,

 

That’s the reference I was thinking the data was probably from. The total number of samples used for genetic analysis in this study was 24 not 114. Can you please look into correcting the summary stats so that the correct frequency is reported for mutations?

 

In looking at the sample names for this study in BioMart, it looks like additional studies were added to the BioMart dataset. Maybe that’s where the n-114 came from. However, that messes up the frequencies as not all the genes were tested in all 114 samples.

 

Many thanks,

Heather

 

From: Elena Rivkin [mailto:[hidden email]]
Sent: Monday, March 21, 2011 9:14 AM
To: Estrella, Heather; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Heather, 

These data were derived from the following publication:

 

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

 

Siân Jones1,* et al

 

Science. 2008 September 26; 321(5897): 1801–1806. doi:10.1126/science.1164368.

 

Elena

 

 

 

From: "Estrella, Heather" <[hidden email]>
Date: Mon, 21 Mar 2011 12:08:21 -0400
To: "[hidden email]" <[hidden email]>
Subject: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Hi,

In looking at the mutation frequencies reported for the Pancreatic Cancer (JHU/US) dataset, it reports the frequencies out of n=114. Can you please send me the reference to the source data behind what’s reported for “Pancreatic Cancer (JHU/US)”?

Thanks,

Heather


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

Estrella, Heather

Thanks Jason,

 

It’s misleading how Biomart reports some of the mutation frequencies as some of the genes were only tested in the 24 samples and not the full 114 so the frequency reported (x/114) is much less than the actual x/24 for that data set.

 

Thanks,
Heather

 

From: Jianxin Wang [mailto:[hidden email]]
Sent: Monday, March 21, 2011 9:44 AM
To: Estrella, Heather; Elena Rivkin; [hidden email]
Subject: RE: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

 

Heather,

 

 

Yes, the 114 samples are from their “discovery” studies (24 samples) and “prevalence” studies (the rest of them).

 

Jason

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Estrella, Heather
Sent: Monday, March 21, 2011 11:38 AM
To: Elena Rivkin; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Thanks Elena,

 

That’s the reference I was thinking the data was probably from. The total number of samples used for genetic analysis in this study was 24 not 114. Can you please look into correcting the summary stats so that the correct frequency is reported for mutations?

 

In looking at the sample names for this study in BioMart, it looks like additional studies were added to the BioMart dataset. Maybe that’s where the n-114 came from. However, that messes up the frequencies as not all the genes were tested in all 114 samples.

 

Many thanks,

Heather

 

From: Elena Rivkin [mailto:[hidden email]]
Sent: Monday, March 21, 2011 9:14 AM
To: Estrella, Heather; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Heather, 

These data were derived from the following publication:

 

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

 

Siân Jones1,* et al

 

Science. 2008 September 26; 321(5897): 1801–1806. doi:10.1126/science.1164368.

 

Elena

 

 

 

From: "Estrella, Heather" <[hidden email]>
Date: Mon, 21 Mar 2011 12:08:21 -0400
To: "[hidden email]" <[hidden email]>
Subject: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Hi,

In looking at the mutation frequencies reported for the Pancreatic Cancer (JHU/US) dataset, it reports the frequencies out of n=114. Can you please send me the reference to the source data behind what’s reported for “Pancreatic Cancer (JHU/US)”?

Thanks,

Heather


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

Jianxin Wang

Heather,

 

I’m not sure what you mean by saying “some of the genes were only tested in the 24 samples”. Can you clarify?

 

Jason

 


From: Estrella, Heather [mailto:[hidden email]]
Sent: Monday, March 21, 2011 1:33 PM
To: Jianxin Wang; Elena Rivkin; [hidden email]
Subject: RE: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

 

Thanks Jason,

 

It’s misleading how Biomart reports some of the mutation frequencies as some of the genes were only tested in the 24 samples and not the full 114 so the frequency reported (x/114) is much less than the actual x/24 for that data set.

 

Thanks,
Heather

 

From: Jianxin Wang [mailto:[hidden email]]
Sent: Monday, March 21, 2011 9:44 AM
To: Estrella, Heather; Elena Rivkin; [hidden email]
Subject: RE: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

 

Heather,

 

 

Yes, the 114 samples are from their “discovery” studies (24 samples) and “prevalence” studies (the rest of them).

 

Jason

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Estrella, Heather
Sent: Monday, March 21, 2011 11:38 AM
To: Elena Rivkin; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Thanks Elena,

 

That’s the reference I was thinking the data was probably from. The total number of samples used for genetic analysis in this study was 24 not 114. Can you please look into correcting the summary stats so that the correct frequency is reported for mutations?

 

In looking at the sample names for this study in BioMart, it looks like additional studies were added to the BioMart dataset. Maybe that’s where the n-114 came from. However, that messes up the frequencies as not all the genes were tested in all 114 samples.

 

Many thanks,

Heather

 

From: Elena Rivkin [mailto:[hidden email]]
Sent: Monday, March 21, 2011 9:14 AM
To: Estrella, Heather; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Heather, 

These data were derived from the following publication:

 

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

 

Siân Jones1,* et al

 

Science. 2008 September 26; 321(5897): 1801–1806. doi:10.1126/science.1164368.

 

Elena

 

 

 

From: "Estrella, Heather" <[hidden email]>
Date: Mon, 21 Mar 2011 12:08:21 -0400
To: "[hidden email]" <[hidden email]>
Subject: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Hi,

In looking at the mutation frequencies reported for the Pancreatic Cancer (JHU/US) dataset, it reports the frequencies out of n=114. Can you please send me the reference to the source data behind what’s reported for “Pancreatic Cancer (JHU/US)”?

Thanks,

Heather


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

Estrella, Heather

Hi Jason,

 

The 90 additional samples only looked for mutations in a subset of 39 genes identified in the original 24 samples. The n=114 should only apply to the frequency calculations for those 39 genes.

 

I couldn’t find in their publication or supplementary material an exact list of the 39 genes, but based on the article, they would be a subset of the ~80 genes reported in Supplementary table 7. Through process of elimination, an example would be CTAG2. You’ll have to contact the authors to determine exactly what 39 genes were measured across all 114 samples.

 

(http://dcc.icgc.org/martreport/?report=gene_report&ensembl_gene_id=ENSG00000126890&datasets=hsapiens_gene_ensembl_tcgaBRCA)

 

Thanks,
Heather

 

From: Jianxin Wang [mailto:[hidden email]]
Sent: Monday, March 21, 2011 12:52 PM
To: Estrella, Heather; Elena Rivkin; [hidden email]
Subject: RE: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

 

Heather,

 

I’m not sure what you mean by saying “some of the genes were only tested in the 24 samples”. Can you clarify?

 

Jason

 


From: Estrella, Heather [mailto:[hidden email]]
Sent: Monday, March 21, 2011 1:33 PM
To: Jianxin Wang; Elena Rivkin; [hidden email]
Subject: RE: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

 

Thanks Jason,

 

It’s misleading how Biomart reports some of the mutation frequencies as some of the genes were only tested in the 24 samples and not the full 114 so the frequency reported (x/114) is much less than the actual x/24 for that data set.

 

Thanks,
Heather

 

From: Jianxin Wang [mailto:[hidden email]]
Sent: Monday, March 21, 2011 9:44 AM
To: Estrella, Heather; Elena Rivkin; [hidden email]
Subject: RE: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

 

Heather,

 

 

Yes, the 114 samples are from their “discovery” studies (24 samples) and “prevalence” studies (the rest of them).

 

Jason

 


From: [hidden email] [mailto:[hidden email]] On Behalf Of Estrella, Heather
Sent: Monday, March 21, 2011 11:38 AM
To: Elena Rivkin; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Thanks Elena,

 

That’s the reference I was thinking the data was probably from. The total number of samples used for genetic analysis in this study was 24 not 114. Can you please look into correcting the summary stats so that the correct frequency is reported for mutations?

 

In looking at the sample names for this study in BioMart, it looks like additional studies were added to the BioMart dataset. Maybe that’s where the n-114 came from. However, that messes up the frequencies as not all the genes were tested in all 114 samples.

 

Many thanks,

Heather

 

From: Elena Rivkin [mailto:[hidden email]]
Sent: Monday, March 21, 2011 9:14 AM
To: Estrella, Heather; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Heather, 

These data were derived from the following publication:

 

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

 

Siân Jones1,* et al

 

Science. 2008 September 26; 321(5897): 1801–1806. doi:10.1126/science.1164368.

 

Elena

 

 

 

From: "Estrella, Heather" <[hidden email]>
Date: Mon, 21 Mar 2011 12:08:21 -0400
To: "[hidden email]" <[hidden email]>
Subject: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Hi,

In looking at the mutation frequencies reported for the Pancreatic Cancer (JHU/US) dataset, it reports the frequencies out of n=114. Can you please send me the reference to the source data behind what’s reported for “Pancreatic Cancer (JHU/US)”?

Thanks,

Heather


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

Elena Rivkin
That you Heather for you input. 
We will review it as soon as possible. 
Elena

From: "Estrella, Heather" <[hidden email]>
Date: Tue, 22 Mar 2011 11:49:38 -0400
To: Jianxin Wang <[hidden email]>, Microsoft Office User <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: RE: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

Hi Jason,

 

The 90 additional samples only looked for mutations in a subset of 39 genes identified in the original 24 samples. The n=114 should only apply to the frequency calculations for those 39 genes.

 

I couldn’t find in their publication or supplementary material an exact list of the 39 genes, but based on the article, they would be a subset of the ~80 genes reported in Supplementary table 7. Through process of elimination, an example would be CTAG2. You’ll have to contact the authors to determine exactly what 39 genes were measured across all 114 samples.

 

(http://dcc.icgc.org/martreport/?report=gene_report&ensembl_gene_id=ENSG00000126890&datasets=hsapiens_gene_ensembl_tcgaBRCA)

 

Thanks,
Heather

 

From: Jianxin Wang [[hidden email]]
Sent: Monday, March 21, 2011 12:52 PM
To: Estrella, Heather; Elena Rivkin; [hidden email]
Subject: RE: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

 

Heather,

 

I’m not sure what you mean by saying “some of the genes were only tested in the 24 samples”. Can you clarify?

 

Jason

 


From: Estrella, Heather [[hidden email]]
Sent: Monday, March 21, 2011 1:33 PM
To: Jianxin Wang; Elena Rivkin; [hidden email]
Subject: RE: [BioMart Users] ICGC BioMart: Pancreatic Cancer(JHU/US)dataset reference

 

Thanks Jason,

 

It’s misleading how Biomart reports some of the mutation frequencies as some of the genes were only tested in the 24 samples and not the full 114 so the frequency reported (x/114) is much less than the actual x/24 for that data set.

 

Thanks,
Heather

 

From: Jianxin Wang [[hidden email]]
Sent: Monday, March 21, 2011 9:44 AM
To: Estrella, Heather; Elena Rivkin; [hidden email]
Subject: RE: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US)dataset reference

 

Heather,

 

 

Yes, the 114 samples are from their “discovery” studies (24 samples) and “prevalence” studies (the rest of them).

 

Jason

 


From:[hidden email] [[hidden email]] On Behalf Of Estrella, Heather
Sent: Monday, March 21, 2011 11:38 AM
To: Elena Rivkin; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Thanks Elena,

 

That’s the reference I was thinking the data was probably from. The total number of samples used for genetic analysis in this study was 24 not 114. Can you please look into correcting the summary stats so that the correct frequency is reported for mutations?

 

In looking at the sample names for this study in BioMart, itlooks like additional studies were added to the BioMart dataset. Maybe that’s where the n-114 came from. However, that messes up the frequencies as not all the genes were tested in all 114 samples.

 

Many thanks,

Heather

 

From: Elena Rivkin[[hidden email]]
Sent: Monday, March 21, 2011 9:14 AM
To: Estrella, Heather; [hidden email]
Subject: Re: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Heather, 

These data were derived from the following publication:

 

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

 

Siân Jones1,* et al

 

Science. 2008 September 26; 321(5897): 1801–1806. doi:10.1126/science.1164368.

 

Elena

 

 

 

From: "Estrella, Heather" <[hidden email]>
Date: Mon, 21 Mar 2011 12:08:21 -0400
To: "[hidden email]" <[hidden email]>
Subject: [BioMart Users] ICGC BioMart: Pancreatic Cancer (JHU/US) dataset reference

 

Hi,

In looking at the mutation frequencies reported for the Pancreatic Cancer (JHU/US) dataset, it reports the frequencies out of n=114. Can you please send me the reference to the source data behind what’s reported for “Pancreatic Cancer (JHU/US)”?

Thanks,

Heather


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users