Question: This Is Different... Showing Lack Of Similarity Between Expression Profiles?
1
gravatar for Johnny R
7.7 years ago by
Johnny R50
Johnny R50 wrote:

It's common to talk about expression similarity with clustering, correlation coefficients, etc. I want to do something slightly different. I want to argue that, biologically, my two samples are very different. I have microarray expression profiles from both. I have shown:

1) Negative Pearson/Spearmann correlations for genome-wide comparisons. 2) The genes differentially expressed in one sample aren't differentially expressed in the other.

This doesn't seem like it's enough. Any suggestions?

ADD COMMENTlink written 7.7 years ago by Johnny R50
1

Not clear what you mean by "genes differentially expressed in one sample aren't differentially expressed in the other." Differential expression means significantly different expression under one condition as compared with another (e.g. cancer versus normal, drug-treated versus control) - i.e. we compare groups of samples. So what are you comparing to what?

ADD REPLYlink written 7.7 years ago by Neilfws48k

I agree with the comment above and also think it would be easier to help you with more details. What are you samples, conditions,... Can you detail a bit more please?

ADD REPLYlink written 7.7 years ago by Philippe1.9k

Need more details, for sure. What type of data? Replicates? What is the experimental design?

ADD REPLYlink written 7.7 years ago by Sean Davis25k
1
gravatar for Gjain
7.7 years ago by
Gjain5.3k
Munich, Germany
Gjain5.3k wrote:

Can you look at the marks(TFs, histone modification marks, CpGislands etc.) your data contains and then may be compare it say expressed genes with specific marks or expressed vs non-expressed genes with a specific or group of specific marks(active chromatin, repressive etc.)

ADD COMMENTlink written 7.7 years ago by Gjain5.3k
1
gravatar for Larry_Parnell
7.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Transcriptional response: With different sets of genes differentially expressed in response to different treatments, one could look for common regulators of the expression of genes in treatment A and in treatment B. For example, many genes in treatment A (to the point of significant enrichment) may be regulated by transcription factors (TFs) X and Y while genes seen after treatment B are preferentially regulated by TFs D and Z.

In other words, try to group your genes into regulatory sets and ask if there is significant enrichment for that assignment for treatment A vs B and for each of those vs the entire genome.

Biological response: You can also move into the biological response. Do the differentially expressed genes elicit a biological response that makes sense with the cell biology and biochemistry also noted for these two treatments? This could be teased out with GO (gene ontology) analysis with a tool like DAVID or g:GOSt.

ADD COMMENTlink written 7.7 years ago by Larry_Parnell16k
0
gravatar for Johnny R
7.7 years ago by
Johnny R0
Johnny R0 wrote:

To clarify - let's say I have sets of microarray data from the treatment of mammalian cells with two different drugs (normalized to untreated controls). From some simple analyses, I suspect that the transcriptional response to these drugs is very different. For instance, the differentially-expressed genes in each treatment are non-overlapping. What else could I look at to demonstrate that these drugs are causing a very different transcriptional response in mammalian cells?

(In response to above): MEFs + Drug A x 3 replicates; MEFs untreated x 3 replicates

MEFs + Drug B x 3 replicates; MEFs untreated x 3 replicates

ADD COMMENTlink written 7.7 years ago by Johnny R0
0
gravatar for xenophiliuslovegood
7.7 years ago by
xenophiliuslovegood150 wrote:

Hi,

what happens quantitatively to the extremes of your expression profile? can you show that some transcript which is strongly expressed under one of the drugs is only weakly, or not at all, expressed under the other treatment? I would go for that as a start.

ADD COMMENTlink written 7.7 years ago by xenophiliuslovegood150
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