Q_Goest said:
I'll try again... So "expressed" genes are 'transcribed' from DNA to mRNA (transcriptome), and then 'translated' from mRNA to protein (proteome). And these 10,000 genes are active when they are going through this process. <do I sound like a biologist yet?> lol
You got the concept and almost sound like a biologist

. However, keep in mind that this is a very simplified concept and that reality is not as clear cut as that.
For example, the study you linked only looked at the transcription and not at expression. As I said before, transcription does not always equate to protein expressed. Also, expression does not necessarly equates to an active protein. So what the researcher meant by active genes were those that were actively transcribed.
Q_Goest said:
Ok, this is strange. I believe I read that some genes can create more than one type of protein. So either the transcription to mRNA or the translation to protein must be able to propogate along more than one path. Is that what you're saying? Isn't the purpose of expressing a gene (in the most simple terms), "to create protein molecules"? And if that's true, then I'm still a bit lost as to what all these proteins are doing. They must interact with other portions of the cell in some way, so I wonder if there's a very simple way of catagorizing the function of these proteins, and hence the expressed gene.
You are right, one gene can produce more than 1 protein. You usually end up characterizing each protein despite the fact that they are coming from the same gene. I'll like to give you a good example but I just can't think of a good one right now. I study bacteria and not eukaryotes. Monique studies eukaryotes so I'm sure she could find an example.
As far as the transcription or translation path is concern, we are getting into the more complex part of expression. For transcription, RNA polymerase can bind to different sites and initiate transcription at different point. Therefore you end up with different mRNA. That one way to produce 2 "different" proteins.
The initial transcription does produce an immature form of mRNA and that immature mRNA must be process prior to translation. Processing of the mRNA into a mature form can produce different mature mRNA and thus produce more than 1 protein. As fas translation goes, it will only produce one protein per mRNA molecules but post-translation processing will produce different form of the protein. There several different post-translation processing and each modification will have an impact of the function of the protein. Again, this is the more complex part of protein expression and function. I am barely scratching the surface.
Q_Goest said:
One other thing strikes me as odd here. With all these proteins floating around, some of them being used to transcribe genes and others with various other functions, it seems strange that these things seem to 'know' what they are doing.
Protein don't float around. Proteins often have specific location and proteins are directed to their location by other proteins. They "know" what to do because they are in the right place and they can interact with other protein or DNA. Those interaction are very specific and therefore limits the type of "jobs" a protein can do.
Q_Goest said:
Why don't all these different molecules end up turning into a pile of goo inside the cell instead of doing what they're supposed to do? Any good references that helps explain that would be appreciated.
Protein will sometime form "pile", at least in bacteria, when protein processing fails or is not under optimal condition. Protein will also be degraded if they are not properly process. The system is far from being perfect and a lot of mistake happens but the cell has mechanism to deal with the mistakes.