Question: T Cell Specific Gene Expression Data
5
gravatar for pixie@bioinfo
7.3 years ago by
pixie@bioinfo1.1k
India
pixie@bioinfo1.1k wrote:

I need to do some interaction studies with genes corresponding to T cell. Is there any database where I can get T cell specific gene expression data ?

gene • 6.7k views
ADD COMMENTlink modified 8 months ago by alexis.vandenbon80 • written 7.3 years ago by pixie@bioinfo1.1k

It's a bit unclear to me whether you are interested in finding genes that are specifically expressed in T cells relative to other tissues and cell types, or whether you are looking for data sets that explore many different conditions and perturbations specifically in T cells.

ADD REPLYlink written 7.3 years ago by Andrew Su4.7k

Actually ...even I am not sure which way I should be going...just trying to think of all the possibilities. The thing is....I have some gene specific information and these experiments have been done on T cells. Now I am thinking of creating networks based on expression data of those genes...

ADD REPLYlink written 7.3 years ago by pixie@bioinfo1.1k
7
gravatar for Neilfws
7.3 years ago by
Neilfws47k
Sydney, Australia
Neilfws47k wrote:

BioGPS include tissue and cell-specific expression data. It has downloadable datasets as well as the web interface. I don't know if there's anything more specific to T cells.

ADD COMMENTlink written 7.3 years ago by Neilfws47k
1

Because there is no universally accepted threshold for "expressed in a sample", we don't provide such lists. However, we do provide the entire data matrix for download (on the "Downloads" page), and from there it's reasonably simple to define your filters in your favorite tool (Excel, R, etc.).

ADD REPLYlink written 7.3 years ago by Andrew Su4.7k

I was looking at BioGPS to download tissue specific data, I can see tissue expression per gene - not sure where I can find the all genes from specific cell or tissue. For example this link gives the expression profile of TNF in different Tissue (http://plugins.gnf.org/cgi-bin/getRawData.cgi?gene=7124&dataset=1) How can I download all genes expressing in a particular tissue from BioGPS ?

ADD REPLYlink written 7.3 years ago by Khader Shameer17k

Thanks Andrew. I will check the downloads page.

ADD REPLYlink written 7.3 years ago by Khader Shameer17k
4
gravatar for Daniel Swan
7.3 years ago by
Daniel Swan13k
Earlham Institute, Norwich, UK
Daniel Swan13k wrote:

There may be some information in this paper: http://www.biomedcentral.com/1471-2164/7/115

"Blood is a complex tissue comprising numerous cell types with distinct functions and corresponding gene expression profiles. We attempted to define the cell type specific gene expression patterns for the major constituent cells of blood, including B-cells, CD4+ T-cells, CD8+ T-cells, lymphocytes and granulocytes. We did this by comparing the global gene expression profiles of purified B-cells, CD4+ T-cells, CD8+ T-cells, granulocytes, and lymphocytes using cDNA microarrays."

The supplementary materials have the gene 'signatures' for the cell types. I'm sure there's other studies of this type, you might also want to crawl GEO and ArrayExpress for relevant microarray experiments and look at the associated publications.

ADD COMMENTlink written 7.3 years ago by Daniel Swan13k
4
gravatar for Wjeck
7.3 years ago by
Wjeck480
Chapel Hill, NC
Wjeck480 wrote:

If you're looking for RNA-seq data, try searching the ncbi short read archive for the following:

"Illumina sequencing of Human CD4 T cells RNA-Seq paired-end library"

There is a ton of data there, I see at least 15 data sets. This might be a bit of a pain to process, but the data are out there.

ADD COMMENTlink written 7.3 years ago by Wjeck480
4
gravatar for Mike Dewar
7.2 years ago by
Mike Dewar1.5k
Columbia University, NYC, USA
Mike Dewar1.5k wrote:

I can reccomend the data sets provided by the Immunological Genome Project (immgen): http://www.immgen.org/ - they have a load of arrays, all using the same SOP, available on GEO here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15907

ADD COMMENTlink written 7.2 years ago by Mike Dewar1.5k
3
gravatar for Philip Zimmermann
7.3 years ago by
Switzerland
Philip Zimmermann40 wrote:

Genevestigator is an online tool that allows you to find which genes are expressed in T cells and not in other tissue types. The tool for this is called Anatomy within the Biomarker Search section of the applications. Genevestigator is freely accessible, and after registration you have full access to all tools for seven days. After that, you will continue to have free access to the basic tools (but this does not include the biomarker search tools). If you need any help, please contact me (phz@nebion.com).

ADD COMMENTlink written 7.3 years ago by Philip Zimmermann40

Thanks for the info...I needed some simple tool/database where I could correlate the expression data of the genes with some other modifications...

ADD REPLYlink written 7.3 years ago by pixie@bioinfo1.1k

BioGPS (linked above in Neil's answer) allows users to search by correlated expression among a reference panel of normal human and mouse tissues.

ADD REPLYlink written 7.3 years ago by Andrew Su4.7k

BioGPS (linked above in Neil's answer) allows users to search by correlated expression among a reference panel of normal human and mouse tissues

ADD REPLYlink written 7.3 years ago by Andrew Su4.7k

BioGPS (linked above in Neil's answer) allows users to search by correlated expression among a reference panel of normal human and mouse tissues...

ADD REPLYlink written 7.3 years ago by Andrew Su4.7k
2
gravatar for Khader Shameer
7.3 years ago by
Manhattan, NY
Khader Shameer17k wrote:

You may also check HPRD, download the raw data files and parse the proteins based on tissue expression. For example see the interleukin 8 at HPRD. You can also get the literature curated interacting partners of IL8 from HPRD.

ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by Khader Shameer17k
2
gravatar for alexis.vandenbon
8 months ago by
alexis.vandenbon80 wrote:

How about the data in our Immuno-Navigator database? You can download it here (for mouse): https://sysimm.ifrec.osaka-u.ac.jp/immuno-navigator/?tab=download

We have 634 samples for CD4+ T cells, and more for specific CD4+ T cell subsets and CD8+ T cells.

All data is from one platform (Affymetrix GeneChip Mouse Genome 430 2.0), with batch effects treated as far as possible. Please see our paper for more details.

If you are interested in human data, I can make them available for download soon.

ADD COMMENTlink written 8 months ago by alexis.vandenbon80

Thanks for sharing, but I hope that OP either fixed his issue or moved on by now ;-)

ADD REPLYlink written 8 months ago by WouterDeCoster21k

Hey, Alexis, Please share the human data. I am sure it would be widely cited. Thanks.

ADD REPLYlink written 8 months ago by Shicheng Guo4.5k
1

I would even recommend adding a Tools post with more information about how to use it- could be very useful. Disclaimer: Alex is in the lab next door.

ADD REPLYlink written 8 months ago by ddiez1.6k

Only three months (!) after your suggestion, I actually made a Tools post!

ADD REPLYlink written 5 months ago by alexis.vandenbon80

Hi Sheldon,

I added the human data to the download page. This data too is all from a single platform, and treated for batch effects.

Alex

ADD REPLYlink written 8 months ago by alexis.vandenbon80
0
gravatar for Marian
6.6 years ago by
Marian0
Marian0 wrote:

i have list of genes for a particular immunological disease.are there tools to find the expression of these genes in all immune cells

ADD COMMENTlink written 6.6 years ago by Marian0
0
gravatar for Shicheng Guo
8 months ago by
Shicheng Guo4.5k
Shicheng Guo4.5k wrote:

I think the best answer is Blueprint Project dataset:

http://epigenomesportal.ca/ihec/grid.html?as=1&i=all&ac=2

BLUEPRINT will focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukaemic counterparts. It aims to generate at least 100 reference epigenomes and study them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease.

ADD COMMENTlink modified 8 months ago • written 8 months ago by Shicheng Guo4.5k
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