Hi,
I am new in the field of cluster analysis of the RNAseq data and would like to ask more experienced guys if the strategy I plan to apply makes any sense.
The hypothesis I want to verify states:
The sorted cells from young knock-out (KO) mice have transcriptome profile resembling the cell from old wild-type (WT) mice.
In other words, I suppose that KO cells show premature aging.
Experiment scheme:
I did RNAseq with 4 groups. 4 samples/group :
1. WT - young
2. WT - old
3. KO - young
4. KO - old
Differential expression done by DEseq2.
Now, does it make sense to use supervised sample-clustering to verify the hypothesis?
I am thinking to select the "classifier genes" by comparing WT young and WT old - to select marker genes for aged phenotyped. I have around 1000 genes significantly changed by DESeq2.
Then, based on this "classifier genes" I want to make supervised clustering (k-mean?) of all WT and KO samples, to see if young KO cell cluster together with old WT cells.
Can I verify my hypothesis by this strategy? If yes, what tools (R packages or other programs) for supervised clustering do you recommend?
I would be grateful for any help nad tips.
Best,
Krzysiek
I am new in the field of cluster analysis of the RNAseq data and would like to ask more experienced guys if the strategy I plan to apply makes any sense.
The hypothesis I want to verify states:
The sorted cells from young knock-out (KO) mice have transcriptome profile resembling the cell from old wild-type (WT) mice.
In other words, I suppose that KO cells show premature aging.
Experiment scheme:
I did RNAseq with 4 groups. 4 samples/group :
1. WT - young
2. WT - old
3. KO - young
4. KO - old
Differential expression done by DEseq2.
Now, does it make sense to use supervised sample-clustering to verify the hypothesis?
I am thinking to select the "classifier genes" by comparing WT young and WT old - to select marker genes for aged phenotyped. I have around 1000 genes significantly changed by DESeq2.
Then, based on this "classifier genes" I want to make supervised clustering (k-mean?) of all WT and KO samples, to see if young KO cell cluster together with old WT cells.
Can I verify my hypothesis by this strategy? If yes, what tools (R packages or other programs) for supervised clustering do you recommend?
I would be grateful for any help nad tips.
Best,
Krzysiek