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 ?
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.).
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 ?
There may be some information in this paper
"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.
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.
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
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).
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.
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.
Only three months (!) after your suggestion, I actually made a Tools post!
i have list of genes for a particular immunological disease.are there tools to find the expression of these genes in all immune cells
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.
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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.
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...