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Table 4 Examples of functional modules identified from Gavin dataset and Krogan_extended dataset by ADM algorithm

From: Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks

Data

set

P-value

Cluster frequency

Gene Ontology term

Predicted functional modules

Gavin

1.23e-28

25 out of 25 genes, 100.0%

transcription from RNA polymerase II promoter

ybr193c ybr253w ycr081w ydr308c ydr443c yer022w ygl025c ygl127c ygl151w ygr104c yhr041c yhr058c ykr095w ylr071c yml007w ymr112c ynl025c ynl236w ynr010w yol051w yol135c yor174w ypl042c ypr070w ypr168w

 

3.91e-28

22 out of 24 genes, 91.7%

mRNA metabolic process

ybl026w ybr055c ybr152w ycr077c ydl098c ydl160c ydr037w ydr378c ydr473c yer112w yer146w ygl173c ygr075c ygr091w yjl124c yjr022w ylr438c-a ymr080c ymr268c ynl147w ynl256w yor308c ypr082c ypr178w

 

1.43e-31

20 out of 24 genes, 83.3%

mRNA splicing, via spliceosome

ybr119w ydl087c ydr235w ydr240c yer029c yfl017w-a ygl049c ygr013w ygr074w yhr086w yil061c yjr084w ykl012w ykl204w ylr147c ylr275w

ylr298c yml046w ymr125w yol139c yor276w ypl178w ypr057w ypr182w

Krogan_extended

2.87e-43

30 out of 40 genes, 75.0%

mitochondrial translation

q0140 yal041w ybl090w ybr006w ybr146w ybr251w ydl045w-a ydr041w ydr124w ydr175c ydr337w ydr347w ydr494w yer050c yer073w ygl129c ygr165w ygr215w yhl004w yhr059w yil070c yil093c yjl063c yjr060w yjr101w yjr113c ykl003c ykl151c ykl155c ymr158w ymr188c ynl081c ynl137c ynl306w ynr036c ynr037c yol143c yor158w ypl013c ypl118w

 

5.52e-32

23 out of 36 genes, 63.9%

mRNA splicing, via spliceosome

ybr119w ydl087c ydr020c ydr122w ydr235w ydr240c ydr243c ydr247w ydr515w yer029c yfl018w-a ygr013w ygr074w yhr086w yhr165c yil061c yir009w yjl188c ykl012w ykl095w ykr019c ylr147c ylr275w ylr298c ylr318w yml046w ymr001c ymr132c ymr157c yor036w yor159c yor305w yor359w ypl213w ypr057w ypr182w

 

1.31e-21

22 out of 35 genes, 62.9%

mRNA metabolic process

ybl026w ybl098w ybr055c ycr077c ydl085c-a ydl121c ydl160c ydr055w ydr378c ydr473c yel015w yer112w yer146w yer172c ygl068w ygl173c ygr091w yhr019c yhr140w yjl013c yjl035c yjl124c yjr022w ykl173w ylr419w ylr438c-a ymr268c ynl092w ynl118c ynl147w ynl240c ynr011c yor308c ypr058w ypr178w