Question: Fisher Exact Test For TFs family
0
gravatar for Kurban
3.6 years ago by
Kurban170
china/Urumqi/xinjiang academy of animal scinces
Kurban170 wrote:

hello everyone,
i have finished differential expression analysis of my RNA-seq data and retrieve the transcripts of transcription factors(TF) from differentially expressed unigenes and non differentially expressed unigenes. then i have categorized those TFs to different TF families. then i realized there are many TFs sequences which blong to the same TF family overly expressed than some other TF families, some parts of my data:

TF_families non_DE_TFs_family_No. DE_TFs_family_No.
AP-2 2 0
ARID 5 2
bHLH 67 8
CG-1 1 1
COE 2 0
CP2 4 0
CSD 4 0
CSL 1 0
CUT 6 1
DDT 1 0
DM 6 0
E2F 3 0
ETS 10 2
Fork_head 22 2

.
.
.
and i wanna find overly expressed TF families in my DE TF sets at treated condition. i saw a several papers analysed this kind of data and they used fisher's exact test for that. i searched some materials about fisher's exact test, but in those example fisher's test used for 2x2 contingency table. here i still have no idea how to use fisher's test to my data. so could anyone explain to me how could i do this?

fisher exact test • 1.1k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Kurban170
3
gravatar for Asaf
3.6 years ago by
Asaf5.5k
Israel
Asaf5.5k wrote:

The two cells you miss are the number of overall TFs and the number of TFs not in the family but DE, then you can put the data for each family in a contingency table like:

  DE not DE
in group A B
not in group C D

 

and you can compute p-value using Fisher's exact test using these tables

ADD COMMENTlink written 3.6 years ago by Asaf5.5k
0
gravatar for Kurban
3.6 years ago by
Kurban170
china/Urumqi/xinjiang academy of animal scinces
Kurban170 wrote:

thanks @Asaf

actually i wanted to add this thanks to by adding comment, but now in china(where i am now) it is heard  to even open biostars home page and it is impossible to comment others response. so i am here thank you  by "add answer" and want to ask u a question.

i used the contingency table as you recommended:

(e.g. for TF family RHD)

  DE not DE
in group 5 6
not in group 87 803

 

the fisher's exact test result for this table is :

 

Left p-value
0.999706420 
Right p-value
0.002804590 
2-Tail p-value
0.002804590 

from the result we can see that Right P-value and 2-Tail p-value is smaler than 0.05, does that mean in treated group TFs transcripts in the transcriptome data, RHD TF family overly expressed? 

which p-value should i use ?

could u explain me some thing about this?

thanks

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Kurban170

Yes, you can say that there are more DE TFs in the RHD family than expected at random. Read a bit about the test, you'll understand what are the right and left p-values (briefly: top left cell is more than expected at random or less, respectively)

ADD REPLYlink written 3.6 years ago by Asaf5.5k
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