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IC from PSAM

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mora:
What does the information content (IC) from logos built from a PSAM matrix mean? how does this differ from IC inferred from a classic PSSM/PWM matrix?

Also, is there any information about how LogoGenerator calculate the IC in bits from the values in the PSAM? I assume it has to be very different from how it is calculated according to classic PWM right? (see link)
https://en.wikipedia.org/wiki/Position_weight_matrix

 

xiangjun:
Hi Mora,

Thanks for your questions.

Regarding the notation PSAM, please refer to the two MatrixREDUCE-related publications:

* "Profiling condition-specific, genome-wide regulation of mRNA stability in yeast." Foat BC, Houshmandi SS, Olivas WM, Bussemaker HJ. Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17675-80. Epub 2005 Nov 29.
* "Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE." Foat BC, Morozov AV, Bussemaker HJ. Bioinformatics. 2006 Jul 15;22(14):e141-9
You may simply take the PSAM logo as an alternative to the classic information content (IC) type. If you want to dig deep in technical details, please refer to the source code. The LogoGenerator program in the REDUCE Suite is just a tool for users to employ, as they see fit. Notably, it has more options just the IC or PSAM logos.

Hope this helps a bit.

Xiang-Jun

mora:
Thanks a lot!! One more question:

How exactly logoGenerator calculates the height of each nucleotide at each position?

your Foat et al 2005 paper says that it "the height of each nucleotide is determined by subtracting the smallest weight for any nucleotide at that position and then dividing by the sum of all four weights".

I replicated this on a PSAM I made and the results were similar, but not identical, to the results obtained by Logo nucleotides (y-axis) height.

Does your LogoGenerator makes any other step other than subtracting the smallest weight? maybe some type of normalization?

Ohh I see in your 2006 papers says that for the affinity logo you used the average right? what about when you used the option -style=bits_info? How nucleotide height is calculated then to approximate bits?

xiangjun:

--- Quote ---How exactly logoGenerator calculates the height of each nucleotide at each position?
--- End quote ---

Check the source code. More specifically, the logo_psam() function in LogoGenerator.c. If you can go over a specific example, step-by-step, I'll be able to help.

As for the specifics in the two articles, Harmen may chime in to make a comment.

Best regards,

Xiang-Jun

mora:
Thanks a lot but I do not know how to read C code.

I am posting an example of a matrix I created using Optimize PSAM and two logos from LogoGenerator. Basically what I want to know if how exactly LogoGenerator translates the PSAM values to nucleotides height in bits and in ddG.


For example: for position 3 G value is 1. How does Logo Generator turns that 1 into a ddD of ~ 3 and ~ 0.6 bits

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