Pathway Analysis with an "ideal environment"

Question

[Mozart]

So as probably some of you may know, I am a musician so not a big expert in bioinformatics stuff. My question may sound strange to you, expert guys. By the way I will try to make myself clear on this: Is there a way to compare your cell-x-data with an x-repository?

I mean, if I am studying a Dendritic Cells or Tregs, presumably they will behave differently in the same conditions. Hope this brief description may help to clarify things.

[GenoMax]

Is there a way to compare your cell-x-data with an x-repository?

While the question is clear in your mind we need more clarification. What kind of data and what type of repository?

Dendritic Cells or Tregs, presumably they will behave differently in the same conditions

Why would the same type of cells behave differently in same conditions? Perhaps this goes back to the previous question. What kind of data are we looking at?

[Mozart]

thanks for your reply and sorry if my question was not so clear.

So basically, an up-regulation of a specific receptor may trigger different downstream effects (pathways) depending on the specific cell phenotype because the cells are different; nothing new, the literature is full of these information. What makes a cell different from another one? That's the point that should be taken into account when we talk about pathway analysis, I presume. It is OK to remove redundancies, narrowing down the list of genes potentially involved in a phenotype/cell behaviour; it is OK to compare the number of your differentially expressed genes with the size of a specific pathway.

Nevertheless, the above mentioned data should be filtered out according to a specific cell background. Does it make any sense to you guys?

[GenoMax]

it is OK to compare the number of your differentially expressed genes with the size of a specific pathway.

Most pathway analysis packages do this already. They will have p-value estimates based on the number of genes in your data compared to the total number known for a pathway.

That said, pathway is an amorphous concept we apply on top of our data. Ultimately all cellular processes are connected in one way or other. We don't have the means/tools to measure changes for everything in real time so we end up taking snapshots in an effort to simplify analysis.

[Mozart]

Thanks so much for clarifying.

[Mozart]

Sorry for upping the post but I honestly think this is an important think we could talk about.