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total number of genes from Venn diagrams not the same as files

I have two files containing genes that show significant differences in expression level between high and low expression lines at two time point. When I did the venn diagrams for the two files the total number of from the venn diagrams don't add up to the total I have for each of the two files. The totals from the venn diagrams are fewer (~100) than the ones in my files. Why? emoticon

thomas

RE: total number of genes from Venn diagrams not the same as files
Answer
7/11/12 2:03 PM as a reply to thomas keat teoh.
Hi Thomas,

it's hard to say without looking at the data itself. Did you specify a significance threshold for the data to be high or low expressed?
Did you check for the missing genes if they have signifcant high or low levels?

This is just a wild guess. If this does not solve the problem I will have to look into it in more detail

Don't hesitate t contact us again
Axel

RE: total number of genes from Venn diagrams not the same as files
Answer
1/7/13 9:37 AM as a reply to Axel Nagel.
Hi dear MapMen team!

I´m recently comparing two experiments (A and emoticon with Medicago truncatula (Mt), I have experienced the same problem as described above. I have a data set of about 23000 genes (up/down expressed as Log2), Venn diagram displayed about 15000. I compared the Annotation List of Mt with the list of my experiment and all genes are listed there.

Furthermore, in the Venn diagram list of MapMan (click in the circles), there is the following comparison:
1. Down regulated in A vs Up regulated in B
2. Down regulated in A and B
3. Up regulated in A vs Down regulated in B

As described above is the Venn analysis? I think I´m doing something wrong, can you help me?

Best regards.

RE: total number of genes from Venn diagrams not the same as files
Answer
1/7/13 11:23 AM as a reply to Ricardo Cabeza.
Hi Ricardo,

did you try to set the threshold to a lower value. All values which have been mapped should be there if a threshold of 0 is chosen. Genes which have values below this threshold (insignificant?) will not be displayed.

You suggestion of how to interprete the diagram is more or less correct. It depends if the threshold is positive or negative.
If the threshold is positive, genes within the circle corresponding to the dataset(see color legend) have a value above the threshold(so upregulated by definition of your threshold as significance level).
If the threshold is negative then we talk about down regulated genes.

Hope that sheds some light
Axel

RE: total number of genes from Venn diagrams not the same as files
Answer
6/15/13 12:54 PM as a reply to thomas keat teoh.
thomas keat teoh:
I have two files containing genes that show significant differences in expression level between high and low expression lines at two time point. When I did the venn diagrams for the two files the total number of from the venn diagrams don't add up to the total I have for each of the two files. The totals from the venn diagrams are fewer (~100) than the ones in my files. Why? emoticon

thomas



Hi Thomas. You probably know it by know as you posted your question some time ago, but the possible answer to what you were struggling with are the duplicates within your list. I had it too - couldnt understand why the total number of genes in Venn diagram would not match the number of genes I had as an input.
All I had to do is just to filter my column of genes for duplicates (in excel) and then the numbers matched instantly with the unique entries displayed in e.g. GeneVenn.


Kat