Computational Biology / Bioinformatics/Genetics Homework help

Question
Hi there,

I need a little help on this question:

I just have no clue where to start.

The following data was obtained from somatic hybrids (mouse-human cell lines A to D) with varying numbers of human chromosomes lost (1 to 5):

http://www.flickr.com/photos/89558373@N03/8148313886/in/photostream

Products of four genes (a to d) were analyzed. Gene products were either absent (N) or present (Y). Use the correlation of the presence or absence of each chromosome (1 to 5) with the presence or absence of each gene product to map genes (a to d) on chromosome numbers 1 to 5.

Thanks so much!

Nick

Hi Nick,

I think this can be solved by simple evidence from two/more data sets for the common occurrence of genes and chromosomes.

From Hybrid cell-line A)
Chr 1 and Chr 3 are present and Genes b and c are identified.
Meaning either {b,c} might be present on either {Chr1, Chr3}

Similarly from  B)

either {a,c} might be present on {Chr1, Chr4, Chr5}

Combining observations frrom A) and B), we can make an inference that gene c which is observed in both
should be present on the chromosome that is present in both. We can unambiguously state that it is Chr1.

=> So, gene c is on Chr1

We cannot yet make any unambiguous inference for genes a and b.

Let's take the other data now.

From C) we can say that genes {a,b,c} might be present on either {Chr1, Chr2, Chr3, Chr4}

We already know about gene c which is also confirmed from this data by the presence of Chr1

Now make a comparison between A) and C)
from A) genes {b,c} can occur on either {Chr1, Chr3}
from C) genes {a,b,c} can occur on either {Chr1, Chr2, Chr3, Chr4}

Since b is common in both data, the chromosome where b is located should also occur in both data.
=> So, b can be on either {Chr1, Chr3}. Still unambiguous.

Let's now observe the last data D).

In the last data set we observe only gene c. This we already confirmed to be on Chr1. So no additional useful information to solve for b.

Similarly for gene we can infer from data B) and data C), based on the presence of common chromosomes.
=> gene a can be either on {Chr1, Chr4}. This is still ambiguous and cannot be ascertained with current data.

=> Since gene d is not observed in any of the data sets, it might not be present on any of the chromosomes 1 to 5.

If this is your homework assignment, my intention to answer was to just tell you the methodology, not to do the homework for you. Hope you will write your homework in your own words.

Computational Biology / Bioinformatics

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Sridhar Acharya Malkaram

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Sequence and Structural Analysis, Next generation sequencing, Illumina, SOLiD, CHiP-sequencing, RNA sequencing, miRNA sequencing analysis, Molecular Dynamics, Protein and Nucleic acid simulations, computational methods, Bioinformatics tools, Biological Databases, Search techniques, Protein comparative modelling, Mutation analysis