Analysing with cummeRbund finding extreme genes.

Question

[Veli Kaan Aydin]

First thanks all guys you showed up when I need help and I need to do one more thing. On the figure below I need to find names of extreme different genes or all if possible(I circle some of them). Or there is a better thing for me if I can show all names on figure. Does anyone know how to do that? Or is there any different programme.

Thanks guys :)

Answer 1

[Chris Evelo]

I have never use cummeRbund but you seem to be looking for the genes that show the largest fold changes in expression.

Simply take your expression calculated data, calculate the fold change if that hasn't been done already and sort it to find the extremes. You will probably want to remove data that give expression values in just one of the 2 samples first (these are on your axes in the graph above).

[Veli Kaan Aydin]

I figure out which ones I need, but I am trying to find what is its name and function. Here it is a line;

How can I find it?

test_id        gene_id        gene                                                          locus                        sample_1    sample_2    status    value_1    value_2    log2(fold_change)    test_stat    p_value      q_value        significant
XLOC_000161    XLOC_000161    AL136221.38,AL137002.19,AL160251.29,AL442125.13,BX537316.2    chr13:112779672-113373994    C1          C2          OK        49.8354    0          -inf                 -nan         5.00E-005    0.000283333    yes

[Chris Evelo]

Assuming these labels mean what they usually mean: Take value_1 and value_2 and divide to get the fold change or take log2(fold_change).

[Veli Kaan Aydin]

I did not understand these gene result is from GenBank and it look meaningless to me and I need to find which genes are different and what are their functions so I use bioDBnet and It really confuse my head because it did not find any conversion until I delete the part after dot and when it gave me it looks like;

so any opinion?

GenBank Nucleotide Accession     Gene Symbol
AL136221                         LAMP1
                                 GRTP1
                                 PCID2
                                 CUL4A

Links in table:

• LAMP1
• GRTP1
• PCID2
• CUL4A