I have spent most of this week trying to transform the gene expression data and implement the equations that Ibrahim came up with to incorporate gene expression data onto edge scores.
I have had several major hold-ups to accomplishing this. The first is pretty simple, I just don’t know how to get the kind of data output I want from the CDF function because the scipy.norm.cdf() function outputs an array and I want a single value for each node.
The biggest issue is that the TCGA data on gene expression and PathLinker use different gene nomenclature systems. The TCGA relies on Ensembl IDs whereas PathLinker relies on UniProt IDs. Originally I tried to convert all the Ensembl IDs to common names to UniProt IDs because I have a file that contains UniProt IDs and common names, and another file that contains Ensembl IDs and common names. However, this didn’t work because a single gene may have multiple common names and may refer to multiple UniProt IDs (for example there are about 20 UniProt IDs that correspond to the HLA-A gene).
Therefore, to avoid the loss of data due to various common names, I tried to make a dictionary of Ensembl IDs directly to UniProt IDs. I was able to obtain a file that contained both UniProt and Ensembl IDs from the HUGO Gene Nomenclature Committee website. However, converting between Ensemble and UniProt came with its own problems. First of all, there are many genes that either only have UniProt IDs or only have Ensembl IDs. 997 genes in the interactome were unable to be converted from one to the other because of this reason. In addition, many of the Ensembl IDs in the TCGA file (over 16,000) don’t line up with any of the Ensembl IDs in the dictionary I constructed. I think this might be because the Ensembl IDs in the TCGA file include version numbers at the end of each ID. The version number is the decimal point at the end of the ID name. For example for the gene, “ENSG00000242268.2”, the “.2” means that this is the 2nd version of that gene. I think one way to fix this problem might be to just take all the version numbers out of the gene name when constructing the dictionary from the TCGA file. However, I can’t figure out how to do this without making the code super slow. If every version number were a single decimal place (ie: .1, .2, .3 … etc), I would just cut off the last two digits of each name which wouldn’t be that slow. However different IDs have different number of decimal places. For example, if I cut off the last two digits of “ENSG00000167578.15” I would still be left with the decimal point. Therefore the only way I can currently think of to get rid of the decimal and everything following it is to use a for-loop that goes through every character in the name and if the character is a decimal point to cut the string there. However, if the program has to go through every letter in every gene name, it’s going to be extremely slow. Maybe something I could do is pre-process the data to create a text file that contains gene IDs without the decimal places so it only has to do it one time and won’t slow the whole code down, but I feel like there has to be a faster way to do it within the program.