Question: Analysing with cummeRbund finding extreme genes.
0
gravatar for Veli Kaan Aydin
5.6 years ago by
Turkey
Veli Kaan Aydin40 wrote:

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 posibble(I circle some of them). Or there is a better thing for me if I can show all names on figure. Doesn anyone know how to do that? Or is there any different programme.

Thanks guys :)


rna-seq cummerbund • 1.4k views
ADD COMMENTlink modified 5.6 years ago by Chris Evelo10.0k • written 5.6 years ago by Veli Kaan Aydin40
0
gravatar for Chris Evelo
5.6 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

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).

ADD COMMENTlink written 5.6 years ago by Chris Evelo10.0k

I figure out which ones I need, but I am trying to find what is its name and funtion. 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
ADD REPLYlink written 5.6 years ago by Veli Kaan Aydin40

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)".   

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Chris Evelo10.0k

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
ADD REPLYlink written 5.6 years ago by Veli Kaan Aydin40
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