Question: Tools for finding tissue specific gene expression "markers"?
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gravatar for arvchi
2.6 years ago by
arvchi50
arvchi50 wrote:

I have a count matrix of gene expression data for several samples, derived from heart tissue (pig). I want to confirm that the gene expression pattern in these samples is consistent with heart tissue.

Is there any database, or other tool, to find genes that are only expressed in this given tissue? Negative markers would be good too, in analogy with the use of positive and negative surface markers in immunohistology. The expected result is to say: "genes x,y are expressed in these samples, therefore the samples are likely derived from heart tissue."

I have checked RefEx database. When I look at heart tissue I get a list of genes, but none of them seems to be specific for heart, or else I am misinterpreting the results.

NOTE: I am aware that databases for pig might not be available, but starting with human and finding homologs is a viable option.

ADD COMMENTlink modified 9 months ago by Shamim Sarhadi210 • written 2.6 years ago by arvchi50
1

A great tool for this would be CellNet from Patrick Cahan's lab, it can classify your samples into a variety of tissues based on gene regulatory networks. But it's only available for human and mouse data so far. However, it includes tools for it to be trained for other species. I understand it may not be feasible for you to use it because getting a good training dataset and doing the training could require a substantial effort you might not be able to justify. But if you had mouse or human data in the future that you'd wanna do the same thing with, this would be a cool way to go. Links to Nature Protocols (2017) and Cell (2014) papers: http://dx.doi.org/10.1038/nprot.2017.022 http://dx.doi.org/10.1016/j.cell.2014.07.020

ADD REPLYlink written 2.6 years ago by jaro.slamecka80

The UCSC genome browser has expression information for human genes, maybe you can download it using table browser and use the data to find the most likely tissue.

ADD REPLYlink written 2.6 years ago by Asaf7.6k

Checked it out. Going through UCSC genome browser means I have to look up every gene manually and see if any gene is uniquely expressed in heart?

ADD REPLYlink written 2.6 years ago by arvchi50

No, you can download all the data using the Table Browser (tools->table browser)

ADD REPLYlink written 2.6 years ago by Asaf7.6k
0
gravatar for Shamim Sarhadi
9 months ago by
IRAN
Shamim Sarhadi210 wrote:

Take a look at GENEVESTIGATOR .

This software characterizes genes by finding out where (tissue specific gene expression profile), when and in response to what they are expressed. You cloud integrating and comparing them with public datasets,and also discover and prioritize your biomarkers according to your search.for a specific tissue gene expression profile.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Shamim Sarhadi210
1

This post lacks detail to be a good answer. Please edit it and add some information on how this tool would help OP with their question.

ADD REPLYlink modified 9 months ago • written 9 months ago by RamRS27k
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