Additional file 3 - The GO enrichment of hubs (degree > 10) for different networks.			
			
Term	PIN-5K	hyperg model-5K	random scores-5K
GO:0032991~macromolecular complex	1.13E-12	7.41E-20	1.21E-16
GO:0005761~mitochondrial ribosome	2.81E-11	1.34E-18	1
GO:0000313~organellar ribosome	2.81E-11	1.34E-18	1
GO:0031980~mitochondrial lumen	4.55E-09	6.73E-14	1
GO:0005759~mitochondrial matrix	4.55E-09	6.73E-14	1
GO:0070013~intracellular organelle lumen	7.71E-09	1.02E-18	3.04E-04
GO:0043233~organelle lumen	7.71E-09	1.02E-18	3.04E-04
GO:0044260~cellular macromolecule metabolic process	2.27E-08	9.54E-11	1.20E-08
GO:0031974~membrane-enclosed lumen	2.89E-08	8.97E-18	0.001245481
GO:0005763~mitochondrial small ribosomal subunit	5.31E-08	4.47E-12	1
GO:0000314~organellar small ribosomal subunit	5.31E-08	4.47E-12	1
GO:0032543~mitochondrial translation	8.30E-08	4.15E-14	1
GO:0043170~macromolecule metabolic process	9.08E-08	3.99E-11	1.26E-07
GO:0007005~mitochondrion organization	1.24E-06	2.03E-09	1
GO:0003735~structural constituent of ribosome	1.98E-06	7.53E-11	1
GO:0010467~gene expression	2.62E-06	4.15E-14	0.073513197
GO:0033279~ribosomal subunit	6.36E-06	1.98E-10	1
GO:0030529~ribonucleoprotein complex	6.50E-06	9.02E-10	0.999999993
GO:0044238~primary metabolic process	9.01E-06	4.06E-08	0.089930129
GO:0044446~intracellular organelle part	1.54E-05	1.05E-08	0.001080458
GO:0044422~organelle part	1.54E-05	1.05E-08	0.001080458
GO:0044237~cellular metabolic process	7.21E-05	8.34E-06	0.409794177
GO:0015935~small ribosomal subunit	1.79E-04	5.07E-07	1
GO:0000177~cytoplasmic exosome (RNase complex)	3.13E-04	1.07E-05	1
GO:0031123~RNA 3'-end processing	5.32E-04	4.15E-13	0.999999335
GO:0044429~mitochondrial part	5.96E-04	2.13E-06	1
GO:0008152~metabolic process	7.06E-04	1.05E-05	0.998799846
GO:0005840~ribosome	9.09E-04	3.76E-07	1
GO:0005198~structural molecule activity	0.001300997	1.18E-06	1
GO:0000176~nuclear exosome (RNase complex)	0.001661878	9.61E-05	1
GO:0000178~exosome (RNase complex)	0.002156922	1.35E-04	1
GO:0044267~cellular protein metabolic process	0.00219244	0.007524325	4.26E-05
GO:0016071~mRNA metabolic process	0.002322338	1.51E-10	0.996535204
GO:0005685~snRNP U1	0.004291445	3.28E-04	1
GO:0003723~RNA binding	0.007648734	6.62E-08	1
GO:0070651~nonfunctional rRNA decay	0.010266124	6.46E-04	1
GO:0016078~tRNA catabolic process	0.010266124	6.46E-04	1
GO:0019538~protein metabolic process	0.010917084	0.01473824	3.38E-04
GO:0005739~mitochondrion	0.013433304	4.08E-04	1
GO:0043928~exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	0.016921879	0.001240343	1
GO:0043634~polyadenylation-dependent ncRNA catabolic process	0.016921879	0.001240343	1
GO:0043633~modification-dependent RNA catabolic process	0.016921879	0.001240343	1
GO:0000459~exonucleolytic trimming during rRNA processing	0.021212535	0.001664921	1
GO:0044424~intracellular part	0.027601144	0.00273021	8.92E-05
GO:0006412~translation	0.029094714	8.50E-06	1
GO:0034645~cellular macromolecule biosynthetic process	0.038027246	2.57E-07	0.002048614
GO:0031126~snoRNA 3'-end processing	0.038709523	9.34E-08	1
GO:0031125~rRNA 3'-end processing	0.038709523	0.003646992	1
GO:0043234~protein complex	0.038965058	0.00103184	5.81E-17
GO:0005622~intracellular	0.040431299	0.004443194	1.89E-05
GO:0009059~macromolecule biosynthetic process	0.041831727	3.05E-07	0.002457379
GO:0005839~proteasome core complex	0.044062242	0.00259724	1
GO:0070003~threonine-type peptidase activity	0.045602158	0.003158489	1
GO:0004298~threonine-type endopeptidase activity	0.045602158	0.003158489	1
GO:0005847~mRNA cleavage and polyadenylation specificity factor complex	0.053590463	3.36E-14	1
GO:0034661~ncRNA catabolic process	0.054851958	0.005754833	1
GO:0016075~rRNA catabolic process	0.054851958	0.005754833	1
GO:0005762~mitochondrial large ribosomal subunit	0.081217519	6.01E-05	1
GO:0000315~organellar large ribosomal subunit	0.081217519	6.01E-05	1
GO:0043231~intracellular membrane-bounded organelle	0.095191276	3.88E-04	0.729272281
GO:0043227~membrane-bounded organelle	0.095191276	3.88E-04	0.729272281
GO:0005849~mRNA cleavage factor complex	0.10334257	6.84E-13	1
GO:0034623~cellular macromolecular complex disassembly	0.119326129	2.04E-08	1
GO:0032984~macromolecular complex disassembly	0.119326129	2.04E-08	1
GO:0022411~cellular component disassembly	0.151543006	3.78E-08	1
GO:0044428~nuclear part	0.15228578	7.25E-04	1.22E-08
GO:0005684~U2-dependent spliceosome	0.173572872	0.003634043	1
GO:0043144~snoRNA processing	0.182740619	3.59E-06	1
GO:0003676~nucleic acid binding	0.236625533	1.89E-04	0.999786196
GO:0043628~ncRNA 3'-end processing	0.246823978	2.93E-07	1
GO:0016070~RNA metabolic process	0.316997859	3.59E-05	0.93611874
GO:0032774~RNA biosynthetic process	0.317770731	2.10E-05	0.999816696
GO:0006996~organelle organization	0.32904845	0.908243286	4.46E-10
GO:0043232~intracellular non-membrane-bounded organelle	0.330274917	0.01741562	3.71E-12
GO:0043228~non-membrane-bounded organelle	0.330274917	0.01741562	3.71E-12
GO:0016074~snoRNA metabolic process	0.346659751	8.15E-07	1
GO:0006378~mRNA polyadenylation	0.400196928	3.47E-10	1
GO:0016043~cellular component organization	0.49547342	0.01938604	2.31E-11
GO:0006397~mRNA processing	0.53041435	4.64E-07	1
GO:0044249~cellular biosynthetic process	0.660031353	1.92E-04	0.981687622
GO:0043631~RNA polyadenylation	0.686013775	7.18E-09	1
GO:0006379~mRNA cleavage	0.686013775	3.06E-07	1
GO:0009058~biosynthetic process	0.764047225	3.27E-04	0.99784109
GO:0006353~transcription termination	0.765616929	1.61E-08	1
GO:0006396~RNA processing	0.786278042	6.51E-05	1
GO:0043624~cellular protein complex disassembly	0.837568457	1.87E-06	1
GO:0043241~protein complex disassembly	0.837568457	1.87E-06	1
GO:0031981~nuclear lumen	0.838380362	4.81E-04	7.90E-09
GO:0005634~nucleus	0.970972761	0.19486736	1.02E-11
GO:0031124~mRNA 3'-end processing	0.988235455	3.10E-08	1
GO:0044451~nucleoplasm part	0.998162134	0.002316062	2.38E-07
GO:0005654~nucleoplasm	0.999962866	0.008092375	6.73E-07
GO:0006350~transcription	0.999999993	0.15114668	4.43E-08
GO:0051276~chromosome organization	1	1	8.32E-20
GO:0050789~regulation of biological process	1	1	1.32E-17
GO:0019222~regulation of metabolic process	1	1	5.67E-17
GO:0060255~regulation of macromolecule metabolic process	1	1	3.43E-16
GO:0080090~regulation of primary metabolic process	1	1	8.51E-16
GO:0051171~regulation of nitrogen compound metabolic process	1	1	1.22E-15
GO:0065007~biological regulation	1	1	1.47E-15
GO:0016570~histone modification	1	1	1.50E-15
GO:0016569~covalent chromatin modification	1	1	1.50E-15
GO:0016568~chromatin modification	1	1	5.04E-15
GO:0043687~post-translational protein modification	1	1	5.33E-15
GO:0006325~chromatin organization	1	1	1.21E-14
GO:0031323~regulation of cellular metabolic process	1	1	1.32E-14
GO:0009889~regulation of biosynthetic process	1	1	1.65E-14
GO:0010556~regulation of macromolecule biosynthetic process	1	1	2.62E-14
GO:0050794~regulation of cellular process	1	1	2.81E-14
GO:0048519~negative regulation of biological process	1	1	3.94E-14
GO:0031326~regulation of cellular biosynthetic process	1	1	1.10E-13
GO:0005694~chromosome	1	1	2.13E-13
GO:0045449~regulation of transcription	1	1	4.42E-13
GO:0010468~regulation of gene expression	1	1	1.55E-12
GO:0044427~chromosomal part	1	1	4.23E-12
GO:0000790~nuclear chromatin	1	1	2.25E-11
GO:0000785~chromatin	1	1	4.99E-11
GO:0010605~negative regulation of macromolecule metabolic process	1	1	1.47E-10
GO:0009892~negative regulation of metabolic process	1	1	1.58E-10
GO:0048523~negative regulation of cellular process	1	1	3.50E-10
GO:0006974~response to DNA damage stimulus	1	1	3.95E-10
GO:0006464~protein modification process	1	1	6.12E-10
GO:0000228~nuclear chromosome	1	1	1.97E-09
GO:0044454~nuclear chromosome part	1	1	2.98E-09
GO:0010629~negative regulation of gene expression	1	1	7.96E-09
GO:0009890~negative regulation of biosynthetic process	1	1	8.81E-09
GO:0043412~biopolymer modification	1	1	1.04E-08
GO:0051172~negative regulation of nitrogen compound metabolic process	1	1	1.34E-08
GO:0010558~negative regulation of macromolecule biosynthetic process	1	1	1.34E-08
GO:0016585~chromatin remodeling complex	1	1	3.18E-08
GO:0016481~negative regulation of transcription	1	1	3.66E-08
GO:0006281~DNA repair	1	1	3.68E-08
GO:0031327~negative regulation of cellular biosynthetic process	1	1	4.27E-08
GO:0000278~mitotic cell cycle	1	1	6.72E-08
GO:0051252~regulation of RNA metabolic process	1	1	2.05E-07
GO:0031324~negative regulation of cellular metabolic process	1	1	2.46E-07
GO:0006259~DNA metabolic process	1	1	3.93E-07
GO:0035267~NuA4 histone acetyltransferase complex	1	1	1.57E-06
GO:0007049~cell cycle	1	1	1.87E-06
GO:0000123~histone acetyltransferase complex	1	1	2.17E-06
GO:0051716~cellular response to stimulus	1	1	7.00E-06
GO:0016573~histone acetylation	1	1	7.58E-06
GO:0043189~H4/H2A histone acetyltransferase complex	1	1	9.88E-06
GO:0005515~protein binding	1	1	1.08E-05
GO:0006473~protein amino acid acetylation	1	1	1.82E-05
GO:0051253~negative regulation of RNA metabolic process	1	1	2.86E-05
GO:0033554~cellular response to stress	1	1	3.44E-05
GO:0050896~response to stimulus	1	1	3.60E-05
GO:0016272~prefoldin complex	1	1	3.98E-05
GO:0006357~regulation of transcription from RNA polymerase II promoter	1	1	9.41E-05
GO:0000812~Swr1 complex	1	1	1.16E-04
GO:0016458~gene silencing	1	1	1.36E-04
GO:0043543~protein amino acid acylation	1	1	2.51E-04
GO:0007021~tubulin complex assembly	1	1	2.65E-04
GO:0006950~response to stress	1	1	5.54E-04
GO:0034641~cellular nitrogen compound metabolic process	1	1	6.13E-04
GO:0034621~cellular macromolecular complex subunit organization	1	0.005399115	7.61E-04
GO:0010529~negative regulation of transposition	1	1	7.70E-04
GO:0006730~one-carbon metabolic process	1	1	0.001294731
GO:0010528~regulation of transposition	1	1	0.00148262
GO:0022403~cell cycle phase	1	1	0.001584704
GO:0008080~N-acetyltransferase activity	1	1	0.001906325
GO:0006807~nitrogen compound metabolic process	1	1	0.002124108
GO:0043486~histone exchange	1	1	0.002971172
GO:0015631~tubulin binding	1	1	0.003085381
GO:0004468~lysine N-acetyltransferase activity	1	1	0.003085381
GO:0004402~histone acetyltransferase activity	1	1	0.003085381
GO:0007067~mitosis	1	1	0.003765926
GO:0000932~cytoplasmic mRNA processing body	1	1	0.004267639
GO:0000087~M phase of mitotic cell cycle	1	1	0.004398
GO:0043933~macromolecular complex subunit organization	1	0.062476354	0.00441557
GO:0016410~N-acyltransferase activity	1	1	0.004769352
GO:0051128~regulation of cellular component organization	1	1	0.00602611
GO:0022402~cell cycle process	1	1	0.006910375
GO:0004674~protein serine/threonine kinase activity	1	1	0.007858574
GO:0000280~nuclear division	1	1	0.007989366
GO:0033558~protein deacetylase activity	1	1	0.009195052
GO:0004407~histone deacetylase activity	1	1	0.009195052