Immunogenic signature in genesset

Question

[Omics data mining]

Hello everyone

I want to predict immunogenic signatures in my gene list. I downloaded immunogenicsignature list from http://software.broadinstitute.org/gsea/msigdb/ and performed enrichment using my gene list. As a result, I am getting enrichment of some of the IDs with fdr 0.05 . IDs list is given below

GSE29949_MICROGLIA_BRAIN_VS_CD8_POS_DC_SPLEEN_DN GSE29618_PDC_VS_MDC_DN GSE21670_UNTREATED_VS_TGFB_TREATED_STAT3_KO_CD4_TCELL_DN GSE17721_0.5H_VS_4H_CPG_BMDC_DN GSE21360_PRIMARY_VS_TERTIARY_MEMORY_CD8_TCELL_DN GSE22611_MUTANT_NOD2_VS_CTRL_TRANSDUCED_HEK293T_CELL_UP GSE24726_WT_VS_E2_2_KO_PDC_DAY4_POST_DELETION_UP GSE37301_MULTIPOTENT_PROGENITOR_VS_GRAN_MONO_PROGENITOR_DN GSE7831_UNSTIM_VS_INFLUENZA_STIM_PDC_4H_UP GSE26488_CTRL_VS_PEPTIDE_INJECTION_OT2_THYMOCYTE_DN GSE29164_DAY3_VS_DAY7_UNTREATED_MELANOMA_UP

How can I make some interpretation from above IDs ?? I am just having diffiulty to understand this result ?? I am looking for just simple explanation of this result.

I will appreciate all the suggestions.

Thank you in advance

Answer 1

[Kevin Blighe]

Hey,

Taking just one example from the above: GSE21360_PRIMARY_VS_TERTIARY_MEMORY_CD8_TCELL_DN:

What it means is that there was some study performed ( by these guys: Repetitive antigen stimulation induces stepwise transcriptome diversification but preserves a core signature of memory CD8(+) T cell differentiation ) where a number of genes were identified as statistically significantly down-regulated in tertiary CD8 memory T-cells when comparing [the tertiary cells] to primary CD8 memory T-cells.

It follows that, through enrichment of your input genes, there was a statistically significant 'overlap' between your genes and those identified as down-regulated in tertiary CD8 memory T-cells in the cited study.

More information here: Gene Set: GSE21360_PRIMARY_VS_TERTIARY_MEMORY_CD8_TCELL_DN

Trust that this helps.

Kevin

[Omics data mining]

Dear Kevin

Thanks for this detail. I am not a bioloigst. Therefore it not easy for me to correlate results with hypothesis, I am working on. Thank you giving a clue here. :)

Archana