Given:
2 samples with bio replicates, along with 1 control
FPKM values for each gene
FPKM values for each isoform of each gene
I am trying to find if proportional alteration of specific isoforms of one particular gene has an effect on proportional alteration of isoforms in other genes.
Example:
Gene A has two isoforms: a, b
In control the ratio of a/b is 5/1.
In sample 1 the ratio is 1/10, with b isoform dominating.
In sample 2 the ratio is 50/1, with a isoform dominating.
I want to find if altered a/b ratio of that one particular gene has an effect on proportional isoform distribution in other genes. Example:
Gene B, with isoforms x, y has x/y ratio of 10/1 in controls. In sample 1, y isoform takes proportionally much more, with x/y being 1/10, in line with the trend for gene A in the same sample. In sample 2, x/y follows the trend for Gene A again, with the ratio being 100/1.
I am trying to figure out a way to look for genes like gene B from the example. I am not interested in changes in gene expression levels, just isoform ratios.
In order to do this, I am considering using k-means clustering of ratios. I would have to calculate a ratio of two major isoforms for each gene in each sample, and simply run k-means on the sets. This would be very limiting, as I would be able to use only 2 isoforms of every gene I am trying to cluster, and would restrict myself to using two major isoforms and their ratios.
Do you have any suggestions? Any software with in-built functions for something like this? Or maybe I am missing something obvious?
I know that CummeRbund has similar functionality, but it is for gene level, not isoform level.
2 samples with bio replicates, along with 1 control
FPKM values for each gene
FPKM values for each isoform of each gene
I am trying to find if proportional alteration of specific isoforms of one particular gene has an effect on proportional alteration of isoforms in other genes.
Example:
Gene A has two isoforms: a, b
In control the ratio of a/b is 5/1.
In sample 1 the ratio is 1/10, with b isoform dominating.
In sample 2 the ratio is 50/1, with a isoform dominating.
I want to find if altered a/b ratio of that one particular gene has an effect on proportional isoform distribution in other genes. Example:
Gene B, with isoforms x, y has x/y ratio of 10/1 in controls. In sample 1, y isoform takes proportionally much more, with x/y being 1/10, in line with the trend for gene A in the same sample. In sample 2, x/y follows the trend for Gene A again, with the ratio being 100/1.
I am trying to figure out a way to look for genes like gene B from the example. I am not interested in changes in gene expression levels, just isoform ratios.
In order to do this, I am considering using k-means clustering of ratios. I would have to calculate a ratio of two major isoforms for each gene in each sample, and simply run k-means on the sets. This would be very limiting, as I would be able to use only 2 isoforms of every gene I am trying to cluster, and would restrict myself to using two major isoforms and their ratios.
Do you have any suggestions? Any software with in-built functions for something like this? Or maybe I am missing something obvious?
I know that CummeRbund has similar functionality, but it is for gene level, not isoform level.
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