[BioC] How to do GO enrichment analysis with GOstats while the gene set with no p values of gene difference expression

zhidong yuan zhidong.yuan at gmail.com
Tue Aug 3 15:11:53 CEST 2010 

Hi everyone.

If I have the predicted target genes of miRNAs with no P values of
difference expression, could I do the functional enrichment analysis of
these target genes with your developed GOstats (R package)?  Some say it
could not do that but I found some do it.


Here are scripts that someone used to do the functional enrichment analysis
of a gene list with no P values of difference expression (
http://hi.baidu.com/ajiang12345/blog/item/84033cf5a70e152dbd310947.html).
But I get the different result from DAVID. Please see it in the attachment
file or please download from
http://www.brsbox.com/filebox/down/fc/121c4cf4bc2658fe63c0b8f7d454abda.
Could tell me what make the difference? And could you tell me how to select
the value of categorySize?

library(org.Hs.eg.db)
library(GOstats)
library(GO.db)

geneIds <- c("10406", "10418", "11082", "1281", "1410",
"157506", "167410", "1906" , "2029", "23091", "2625" , "2823" ,
"2877", "2993", "3039" , "3043", "3046", "3283", "3553",
"4015", "4069", "4258", "4345", "4353", "4885", "4886",
"5021", "5055", "5151", "5156", "5320", "5553", "55885",
"56667", "5788" , "5999", "6005", "629",    "6507", "653145",
"6590", "673",    "6876", "695",    "7026", "7070", "7103",
"7412", "760",    "7738", "800",    "828",    "83890", "945", "963")

univ <- Lkeys(org.Hs.egGO)
param <- new("GOHyperGParams", geneIds = geneIds,
universeGeneIds=univ, annotation="org.Hs.eg.db", ontology="BP")
hyp <- hyperGTest(param)
result<-summary(hyp,categorySize=2000)

hist(pvalues(hyp), breaks=50, col="mistyrose")

write.table(result,file="result-all-3-geneid-BP.txt",sep="\t")

----------------------------------------------------

The result I get is :
GOBPID      Pvalue OddsRatio ExpCount Count
Size                                Term
1 GO:0032501 0.0001568145 3.021968 11.976486    24 3438    multicellular
organismal process
2 GO:0032502 0.0012459810 2.626265 10.297409    20 2956
developmental process
3 GO:0007275 0.0051457709 2.457897 7.517527    15 2158 multicellular
organismal development
4 GO:0007154 0.0061081457 2.187407 13.418681    22 3852
cell communication

-- 
Zhidong
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Annotation Cluster 1	Enrichment Score: 3.6053856252516914
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0043627~response to estrogen stimulus	7	12.962962962962962	1.378612119569747E-6	1410,2625,760,5156,5021,3553,4886	47	105	13528	19.1886524822695	0.0014657690160471137	7.331532648784389E-4	0.002195364083090734
GOTERM_BP_FAT	GO:0048545~response to steroid hormone stimulus	8	14.814814814814813	3.484745441921204E-6	1410,2625,760,5156,5021,3553,4886,4015	47	192	13528	11.99290780141844	0.003700910298128468	0.001235161762491277	0.005549178509367536
GOTERM_BP_FAT	GO:0032355~response to estradiol stimulus	5	9.25925925925926	3.267552066770207E-5	1410,5156,5021,3553,4886	47	54	13528	26.65090622537431	0.03416988247807051	0.008654165748880338	0.05202182143972944
GOTERM_BP_FAT	GO:0009725~response to hormone stimulus	8	14.814814814814813	2.1956417137320897E-4	1410,2625,760,5156,5021,3553,4886,4015	47	367	13528	6.274218795292481	0.20835476963210953	0.045653423523490666	0.3490751824817617
GOTERM_BP_FAT	GO:0009719~response to endogenous stimulus	8	14.814814814814813	3.9940341889720306E-4	1410,2625,760,5156,5021,3553,4886,4015	47	405	13528	5.685526661413186	0.3462629853021123	0.046129910985666434	0.6341423786636047
GOTERM_BP_FAT	GO:0010033~response to organic substance	10	18.51851851851852	6.143711138201849E-4	1410,1281,2625,760,5156,5021,3553,4886,629,4015	47	721	13528	3.9920913624693837	0.47998194756114987	0.057712363778680165	0.973889660724514
GOTERM_BP_FAT	GO:0051240~positive regulation of multicellular organismal process	6	11.11111111111111	0.0013740139743678367	760,5021,3553,6507,4886,1906	47	244	13528	7.077781653296127	0.7684492391475862	0.09922238188647736	2.165771834172592
GOTERM_BP_FAT	GO:0060341~regulation of cellular localization	5	9.25925925925926	0.009843658618997714	1410,5021,3553,4886,1906	47	248	13528	5.803019903912149	0.9999731580101143	0.1969049055873272	14.575146171946063
GOTERM_BP_FAT	GO:0051046~regulation of secretion	4	7.4074074074074066	0.031127337352047094	5021,3553,4886,1906	47	202	13528	5.699599747208763	0.9999999999999976	0.35770605094996255	39.563051950229486

Annotation Cluster 2	Enrichment Score: 2.456691639484199
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0002683~negative regulation of immune system process	4	7.4074074074074066	0.0027953729402302985	1281,7070,2877,5788	47	83	13528	13.871315047423737	0.9491279528532574	0.13836375239097942	4.359859205012184
GOTERM_BP_FAT	GO:0050777~negative regulation of immune response	3	5.555555555555555	0.0032286626237957457	1281,2877,5788	47	25	13528	34.53957446808511	0.967962708812792	0.14478509144469376	5.019481915819279
GOTERM_BP_FAT	GO:0048585~negative regulation of response to stimulus	4	7.4074074074074066	0.004725662030567938	1281,2877,3553,5788	47	100	13528	11.513191489361702	0.9935263974929746	0.1416367967579798	7.265788187762134

Annotation Cluster 3	Enrichment Score: 1.9985392847515948
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0009617~response to bacterium	5	9.25925925925926	0.00410497989609644	5553,5320,2877,3553,4069	47	193	13528	7.4567302392239005	0.9874330870579516	0.14470623245084535	6.340541407642764
GOTERM_BP_FAT	GO:0006952~defense response	8	14.814814814814813	0.004430763812887888	5553,2625,5320,4353,3553,629,5788,4069	47	615	13528	3.7441273136135615	0.9911275800631262	0.13726718885790923	6.827258730733088
GOTERM_BP_FAT	GO:0042742~defense response to bacterium	3	5.555555555555555	0.05553829092965229	5553,5320,4069	47	112	13528	7.709726443768996	1.0	0.46225918731051696	59.74494536480752

Annotation Cluster 4	Enrichment Score: 1.8761057400705479
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0042060~wound healing	6	11.11111111111111	4.5629335808404373E-4	653145,1281,5156,3553,4015,5055	47	191	13528	9.041773420964686	0.38467637559628864	0.04740047867029662	0.724160644743066
GOTERM_BP_FAT	GO:0030198~extracellular matrix organization	3	5.555555555555555	0.04867266146190952	1281,5156,4015	47	104	13528	8.302782324058919	1.0	0.4384589919647325	54.823431373163075
GOTERM_BP_FAT	GO:0043062~extracellular structure organization	3	5.555555555555555	0.10596282743693812	1281,5156,4015	47	163	13528	5.297480746638819	1.0	0.6420575403614808	83.1981809967029

Annotation Cluster 5	Enrichment Score: 1.5689404654603825
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0032355~response to estradiol stimulus	5	9.25925925925926	3.267552066770207E-5	1410,5156,5021,3553,4886	47	54	13528	26.65090622537431	0.03416988247807051	0.008654165748880338	0.05202182143972944
GOTERM_BP_FAT	GO:0007243~protein kinase cascade	8	14.814814814814813	2.3077972847647784E-4	695,1410,5999,673,5021,3553,1906,5788	47	370	13528	6.223346751006325	0.21774771032311646	0.04010335480012295	0.3668755973940119
GOTERM_BP_FAT	GO:0000165~MAPKKK cascade	6	11.11111111111111	3.8455483734122593E-4	1410,5999,673,5021,3553,5788	47	184	13528	9.385753931544865	0.3358485316635216	0.04986920989542076	0.6106345390234802
GOTERM_BP_FAT	GO:0051480~cytosolic calcium ion homeostasis	5	9.25925925925926	6.765802114709688E-4	5021,3553,4886,1906,5788	47	118	13528	12.196177425171296	0.5133085763079872	0.05824527512809041	1.0720051854555046
GOTERM_BP_FAT	GO:0051240~positive regulation of multicellular organismal process	6	11.11111111111111	0.0013740139743678367	760,5021,3553,6507,4886,1906	47	244	13528	7.077781653296127	0.7684492391475862	0.09922238188647736	2.165771834172592
GOTERM_BP_FAT	GO:0001568~blood vessel development	6	11.11111111111111	0.0013991087006320069	1281,7070,7026,3553,1906,4015	47	245	13528	7.048892748588797	0.7745583749666964	0.09454068608062627	2.2049151773433695
GOTERM_BP_FAT	GO:0001944~vasculature development	6	11.11111111111111	0.0015568683718070442	1281,7070,7026,3553,1906,4015	47	251	13528	6.880393320335678	0.8094420192730993	0.09842534079377785	2.450656439676402
GOTERM_BP_FAT	GO:0050870~positive regulation of T cell activation	4	7.4074074074074066	0.002174548048344717	7412,7070,3553,5788	47	76	13528	15.148936170212766	0.9013560546074315	0.1273749566393726	3.4072544389836423
GOTERM_BP_FAT	GO:0003012~muscle system process	5	9.25925925925926	0.00249491605249053	1410,800,5021,3553,1906	47	168	13528	8.566362715298887	0.9299052715750058	0.13054602416202687	3.899937668778064
GOTERM_BP_FAT	GO:0006469~negative regulation of protein kinase activity	4	7.4074074074074066	0.003194389410038875	7070,5999,3553,5788	47	87	13528	13.233553436047933	0.9667689471884284	0.14965073997167333	4.967461455567756
GOTERM_BP_FAT	GO:0006874~cellular calcium ion homeostasis	5	9.25925925925926	0.0033950290184059147	5021,3553,4886,1906,5788	47	183	13528	7.864201836995698	0.9731759589616591	0.14557299652337385	5.271616661116363
GOTERM_BP_FAT	GO:0046888~negative regulation of hormone secretion	3	5.555555555555555	0.003490170556399395	3553,4886,1906	47	26	13528	33.211129296235676	0.9757669296843273	0.1435861441323516	5.4155252824941265
GOTERM_BP_FAT	GO:0033673~negative regulation of kinase activity	4	7.4074074074074066	0.003515474473020927	7070,5999,3553,5788	47	90	13528	12.792434988179668	0.9764128933182642	0.13919062769359403	5.453764822247131
GOTERM_BP_FAT	GO:0055074~calcium ion homeostasis	5	9.25925925925926	0.0037385317809496567	5021,3553,4886,1906,5788	47	188	13528	7.65504753282028	0.9814122396557614	0.14210959570286352	5.790225079561118
GOTERM_BP_FAT	GO:0051348~negative regulation of transferase activity	4	7.4074074074074066	0.004215311139247962	7070,5999,3553,5788	47	96	13528	11.99290780141844	0.9888305256772203	0.14357214536737806	6.505641197653778
GOTERM_BP_FAT	GO:0006875~cellular metal ion homeostasis	5	9.25925925925926	0.004336158558686266	5021,3553,4886,1906,5788	47	196	13528	7.34259661311333	0.9901836363425812	0.14283383196952992	6.68616439343136
GOTERM_BP_FAT	GO:0051251~positive regulation of lymphocyte activation	4	7.4074074074074066	0.004339572548517443	7412,7070,3553,5788	47	97	13528	11.86926957666155	0.9902193842413354	0.138663000455445	6.691259500878266
GOTERM_BP_FAT	GO:0008217~regulation of blood pressure	4	7.4074074074074066	0.004725662030567938	5021,3043,4886,1906	47	100	13528	11.513191489361702	0.9935263974929746	0.1416367967579798	7.265788187762134
GOTERM_BP_FAT	GO:0055065~metal ion homeostasis	5	9.25925925925926	0.005082296688643103	5021,3553,4886,1906,5788	47	205	13528	7.020238713025428	0.9955788340807771	0.14738870289773276	7.7935388060866195
GOTERM_BP_FAT	GO:0002696~positive regulation of leukocyte activation	4	7.4074074074074066	0.0055587233688054495	7412,7070,3553,5788	47	106	13528	10.861501405058208	0.9973441255563928	0.15189385594326132	8.494167578085266
GOTERM_BP_FAT	GO:0007204~elevation of cytosolic calcium ion concentration	4	7.4074074074074066	0.006160112237811897	5021,3553,1906,5788	47	110	13528	10.466537717601547	0.9986046786151767	0.1628003583141987	9.37144132014065
GOTERM_BP_FAT	GO:0050867~positive regulation of cell activation	4	7.4074074074074066	0.0063163025619756685	7412,7070,3553,5788	47	111	13528	10.372244585010543	0.9988195507891418	0.1625698103195502	9.597990479213536
GOTERM_BP_FAT	GO:0030005~cellular di-, tri-valent inorganic cation homeostasis	5	9.25925925925926	0.0072591063841199975	5021,3553,4886,1906,5788	47	227	13528	6.339863154934858	0.9995700575270345	0.18025799725260871	10.95426607178307
GOTERM_BP_FAT	GO:0050863~regulation of T cell activation	4	7.4074074074074066	0.007303237139887878	7412,7070,3553,5788	47	117	13528	9.840334606292053	0.9995899201503985	0.17714803471243912	11.017280999251245
GOTERM_BP_FAT	GO:0042102~positive regulation of T cell proliferation	3	5.555555555555555	0.007737575730714262	7412,3553,5788	47	39	13528	22.14075286415712	0.9997425787519741	0.18256215341645043	11.635253290850478
GOTERM_BP_FAT	GO:0048584~positive regulation of response to stimulus	5	9.25925925925926	0.008303503117750438	7070,5320,3553,629,5788	47	236	13528	6.098088712585648	0.9998597118539159	0.18642829370718272	12.434415083022888
GOTERM_BP_FAT	GO:0006873~cellular ion homeostasis	6	11.11111111111111	0.008503489992771469	5021,3553,4886,1906,5788,6005	47	374	13528	4.617590169530094	0.9998868053212374	0.18658115918802154	12.715198636865422
GOTERM_BP_FAT	GO:0002684~positive regulation of immune system process	5	9.25925925925926	0.008548312051515175	7412,7070,3553,629,5788	47	238	13528	6.046844269622742	0.9998921211989658	0.18371272819494178	12.77801339155965
GOTERM_BP_FAT	GO:0055066~di-, tri-valent inorganic cation homeostasis	5	9.25925925925926	0.008672478909057592	5021,3553,4886,1906,5788	47	239	13528	6.0215436659841535	0.9999055805190263	0.18247444089238318	12.95180276203225
GOTERM_BP_FAT	GO:0055082~cellular chemical homeostasis	6	11.11111111111111	0.009073995132663944	5021,3553,4886,1906,5788,6005	47	380	13528	4.54468085106383	0.9999386429886982	0.18645779297609344	13.511563582804353
GOTERM_BP_FAT	GO:0060341~regulation of cellular localization	5	9.25925925925926	0.009843658618997714	1410,5021,3553,4886,1906	47	248	13528	5.803019903912149	0.9999731580101143	0.1969049055873272	14.575146171946063
GOTERM_BP_FAT	GO:0030003~cellular cation homeostasis	5	9.25925925925926	0.010679167914689685	5021,3553,4886,1906,5788	47	254	13528	5.665940693583515	0.9999890671861008	0.20795541028229958	15.715837448750547
GOTERM_BP_FAT	GO:0051051~negative regulation of transport	4	7.4074074074074066	0.010790674263960924	1410,3553,4886,1906	47	135	13528	8.52828999211978	0.9999903027870506	0.20616007255274882	15.866988827190532
GOTERM_BP_FAT	GO:0043405~regulation of MAP kinase activity	4	7.4074074074074066	0.012133625384494631	5999,3553,1906,5788	47	141	13528	8.165384035008298	0.9999977149906135	0.22484248719937894	17.66757142777258
GOTERM_BP_FAT	GO:0050801~ion homeostasis	6	11.11111111111111	0.012209701588018072	5021,3553,4886,1906,5788,6005	47	409	13528	4.222441866514071	0.999997894763788	0.22226309354645846	17.76848298860574
GOTERM_BP_FAT	GO:0050778~positive regulation of immune response	4	7.4074074074074066	0.013080101517659242	7070,3553,629,5788	47	145	13528	7.94013206162876	0.999999175961806	0.23227346112692293	18.914808409997175
GOTERM_BP_FAT	GO:0051249~regulation of lymphocyte activation	4	7.4074074074074066	0.013817031240232466	7412,7070,3553,5788	47	148	13528	7.779183438757906	0.9999996277986609	0.23977817749857977	19.873626829836844
GOTERM_BP_FAT	GO:0043086~negative regulation of catalytic activity	5	9.25925925925926	0.014304720620881712	7070,5999,3553,4886,5788	47	277	13528	5.19548352408019	0.9999997801087367	0.2432555649983149	20.50230484287382
GOTERM_BP_FAT	GO:0051094~positive regulation of developmental process	5	9.25925925925926	0.01447802006172801	5320,760,5021,3553,5788	47	278	13528	5.176794734425226	0.999999817627704	0.24201610231653825	20.724588870757145
GOTERM_BP_FAT	GO:0050671~positive regulation of lymphocyte proliferation	3	5.555555555555555	0.01498219460435864	7412,3553,5788	47	55	13528	15.69980657640232	0.9999998941959841	0.2455632339407936	21.367964864447085
GOTERM_BP_FAT	GO:0051048~negative regulation of secretion	3	5.555555555555555	0.01498219460435864	3553,4886,1906	47	55	13528	15.69980657640232	0.9999998941959841	0.2455632339407936	21.367964864447085
GOTERM_BP_FAT	GO:0006936~muscle contraction	4	7.4074074074074066	0.015097128450717525	1410,800,5021,1906	47	153	13528	7.524961757752747	0.999999906549528	0.2435101083073692	21.513945146759283
GOTERM_BP_FAT	GO:0007267~cell-cell signaling	7	12.962962962962962	0.015381673037560162	945,5021,3553,6507,4258,4885,1906	47	600	13528	3.3580141843971627	0.9999999312833909	0.24387383536774043	21.8742601134708
GOTERM_BP_FAT	GO:0032946~positive regulation of mononuclear cell proliferation	3	5.555555555555555	0.015503790715532016	7412,3553,5788	47	56	13528	15.419452887537991	0.9999999397790844	0.24201178062210515	22.028420146766024
GOTERM_BP_FAT	GO:0070665~positive regulation of leukocyte proliferation	3	5.555555555555555	0.015503790715532016	7412,3553,5788	47	56	13528	15.419452887537991	0.9999999397790844	0.24201178062210515	22.028420146766024
GOTERM_BP_FAT	GO:0055080~cation homeostasis	5	9.25925925925926	0.0159127623351669	5021,3553,4886,1906,5788	47	286	13528	5.031989287308437	0.999999961296523	0.24405934151141961	22.542627891321864
GOTERM_BP_FAT	GO:0001775~cell activation	5	9.25925925925926	0.01609819734561397	7412,1281,5156,1906,5788	47	287	13528	5.014456223589592	0.9999999683284977	0.24309209147866861	22.774730084765093
GOTERM_BP_FAT	GO:0002694~regulation of leukocyte activation	4	7.4074074074074066	0.018731460191989586	7412,7070,3553,5788	47	166	13528	6.9356575237118685	0.9999999981706396	0.269746871350535	26.001131581332615
GOTERM_BP_FAT	GO:0042129~regulation of T cell proliferation	3	5.555555555555555	0.018794136084736	7412,3553,5788	47	62	13528	13.927247769389156	0.9999999982908364	0.2669733771539826	26.076363073292786
GOTERM_BP_FAT	GO:0019725~cellular homeostasis	6	11.11111111111111	0.020384113743819134	5021,3553,4886,1906,5788,6005	47	466	13528	3.705962925760204	0.999999999695637	0.2825213751673976	27.961050550550137
GOTERM_BP_FAT	GO:0044057~regulation of system process	5	9.25925925925926	0.02052817172198247	5021,3553,6507,4886,1906	47	309	13528	4.657439922880948	0.9999999997397241	0.2806391864426714	28.12956660317083
GOTERM_BP_FAT	GO:0046883~regulation of hormone secretion	3	5.555555555555555	0.021136749134292396	3553,4886,1906	47	66	13528	13.083172147001934	0.9999999998656512	0.2841418602066095	28.83739922883691
GOTERM_BP_FAT	GO:0050865~regulation of cell activation	4	7.4074074074074066	0.021508535102179833	7412,7070,3553,5788	47	175	13528	6.578966565349544	0.9999999999103206	0.28486695376712123	29.266600720109125
GOTERM_BP_FAT	GO:0007242~intracellular signaling cascade	10	18.51851851851852	0.023683624485798895	695,1410,828,5999,673,5021,3553,4886,1906,5788	47	1256	13528	2.2916384333920585	0.9999999999915983	0.3053329172520969	31.729372003734856
GOTERM_BP_FAT	GO:0003013~circulatory system process	4	7.4074074074074066	0.025194189693060386	5021,3043,4886,1906	47	186	13528	6.189887897506291	0.9999999999983824	0.31777485892316704	33.392189377481685
GOTERM_BP_FAT	GO:0008015~blood circulation	4	7.4074074074074066	0.025194189693060386	5021,3043,4886,1906	47	186	13528	6.189887897506291	0.9999999999983824	0.31777485892316704	33.392189377481685
GOTERM_BP_FAT	GO:0044092~negative regulation of molecular function	5	9.25925925925926	0.026400273582561043	7070,5999,3553,4886,5788	47	334	13528	4.308829150210218	0.9999999999995667	0.32657571862229495	34.69250348286309
GOTERM_BP_FAT	GO:0048878~chemical homeostasis	6	11.11111111111111	0.029146766859380096	5021,3553,4886,1906,5788,6005	47	512	13528	3.3730053191489358	0.9999999999999786	0.3502309109666104	37.56534268789936
GOTERM_BP_FAT	GO:0045859~regulation of protein kinase activity	5	9.25925925925926	0.029274644676624075	7070,5999,3553,1906,5788	47	345	13528	4.171446191797718	0.9999999999999813	0.34767086447265705	37.69617333034745
GOTERM_BP_FAT	GO:0051046~regulation of secretion	4	7.4074074074074066	0.031127337352047094	5021,3553,4886,1906	47	202	13528	5.699599747208763	0.9999999999999976	0.35770605094996255	39.563051950229486
GOTERM_BP_FAT	GO:0050670~regulation of lymphocyte proliferation	3	5.555555555555555	0.032337139153753365	7412,3553,5788	47	83	13528	10.403486285567801	0.9999999999999993	0.36135176803925684	40.75368203072832
GOTERM_BP_FAT	GO:0043549~regulation of kinase activity	5	9.25925925925926	0.03261647217676452	7070,5999,3553,1906,5788	47	357	13528	4.031229513081828	0.9999999999999996	0.3602091456911336	41.025446843073965
GOTERM_BP_FAT	GO:0032944~regulation of mononuclear cell proliferation	3	5.555555555555555	0.03305531203356653	7412,3553,5788	47	84	13528	10.279635258358661	0.9999999999999997	0.36049829872870176	41.45003845749663
GOTERM_BP_FAT	GO:0070663~regulation of leukocyte proliferation	3	5.555555555555555	0.03305531203356653	7412,3553,5788	47	84	13528	10.279635258358661	0.9999999999999997	0.36049829872870176	41.45003845749663
GOTERM_BP_FAT	GO:0048514~blood vessel morphogenesis	4	7.4074074074074066	0.034761298236376414	7070,7026,3553,1906	47	211	13528	5.456488857517394	1.0	0.36462765825838994	43.07357025606334
GOTERM_BP_FAT	GO:0042493~response to drug	4	7.4074074074074066	0.036871751553382556	5021,3553,6507,4015	47	216	13528	5.330181245074862	1.0	0.3786558732594951	45.023648717288765
GOTERM_BP_FAT	GO:0051338~regulation of transferase activity	5	9.25925925925926	0.03709923269083745	7070,5999,3553,1906,5788	47	372	13528	3.868679935941432	1.0	0.3770123718490681	45.23006351338974
GOTERM_BP_FAT	GO:0009968~negative regulation of signal transduction	4	7.4074074074074066	0.03904720936773417	7070,5999,3553,5788	47	221	13528	5.20958890921344	1.0	0.389074599551271	46.96814117862471
GOTERM_BP_FAT	GO:0051050~positive regulation of transport	4	7.4074074074074066	0.039935509894814834	7070,5021,3553,1906	47	223	13528	5.162866138727221	1.0	0.39251437041170123	47.74344219714266
GOTERM_BP_FAT	GO:0042592~homeostatic process	7	12.962962962962962	0.04054382950334111	2877,5021,3553,4886,1906,5788,6005	47	751	13528	2.682834235204125	1.0	0.393727869349376	48.26823618544602
GOTERM_BP_FAT	GO:0002253~activation of immune response	3	5.555555555555555	0.04057411197247147	7070,629,5788	47	94	13528	9.186057039384336	1.0	0.39053935306730736	48.29423120058425
GOTERM_BP_FAT	GO:0043406~positive regulation of MAP kinase activity	3	5.555555555555555	0.047008787380659015	3553,1906,5788	47	102	13528	8.465581977471839	1.0	0.430490544557542	53.548608364016246
GOTERM_BP_FAT	GO:0042127~regulation of cell proliferation	7	12.962962962962962	0.049066806466347965	7412,5320,5156,945,3553,1906,5788	47	787	13528	2.5601124658682313	1.0	0.4376362899497581	55.12057472194013
GOTERM_BP_FAT	GO:0008284~positive regulation of cell proliferation	5	9.25925925925926	0.05147308759984519	7412,5156,3553,1906,5788	47	414	13528	3.476205159831432	1.0	0.4501785790747824	56.8952985069815
GOTERM_BP_FAT	GO:0010648~negative regulation of cell communication	4	7.4074074074074066	0.051899800394626244	7070,5999,3553,5788	47	248	13528	4.642415923129719	1.0	0.449487143624119	57.203065629868775
GOTERM_BP_FAT	GO:0043408~regulation of MAPKKK cascade	3	5.555555555555555	0.05292504428385492	3553,1906,5788	47	109	13528	7.921920749560803	1.0	0.45265657521815994	57.93412637067683
GOTERM_BP_FAT	GO:0010564~regulation of cell cycle process	3	5.555555555555555	0.0573054956530903	3553,1906,5788	47	114	13528	7.574468085106383	1.0	0.4629594167836182	60.927818589411096
GOTERM_BP_FAT	GO:0051173~positive regulation of nitrogen compound metabolic process	6	11.11111111111111	0.06631433228738538	5156,7026,3553,3043,1906,5788	47	644	13528	2.68164398044139	1.0	0.5077675296841472	66.46815034657382
GOTERM_BP_FAT	GO:0042325~regulation of phosphorylation	5	9.25925925925926	0.07297204387090589	7070,5999,3553,1906,5788	47	466	13528	3.088302438133504	1.0	0.5393889521440735	70.07969474109778
GOTERM_BP_FAT	GO:0050804~regulation of synaptic transmission	3	5.555555555555555	0.07796882538600976	5021,6507,1906	47	136	13528	6.349186483103879	1.0	0.5607058038704307	72.54715556320109
GOTERM_BP_FAT	GO:0019220~regulation of phosphate metabolic process	5	9.25925925925926	0.08182477759907406	7070,5999,3553,1906,5788	47	485	13528	2.9673173941653874	1.0	0.57552056619956	74.31947059303647
GOTERM_BP_FAT	GO:0051174~regulation of phosphorus metabolic process	5	9.25925925925926	0.08182477759907406	7070,5999,3553,1906,5788	47	485	13528	2.9673173941653874	1.0	0.57552056619956	74.31947059303647
GOTERM_BP_FAT	GO:0007155~cell adhesion	6	11.11111111111111	0.08768252633814311	7412,1281,7070,945,10418,5788	47	700	13528	2.467112462006079	1.0	0.5917122118064031	76.80788806171898
GOTERM_BP_FAT	GO:0022610~biological adhesion	6	11.11111111111111	0.08809410048996613	7412,1281,7070,945,10418,5788	47	701	13528	2.463593043372689	1.0	0.590166440541759	76.97394227050434
GOTERM_BP_FAT	GO:0051969~regulation of transmission of nerve impulse	3	5.555555555555555	0.08905887621540617	5021,6507,1906	47	147	13528	5.874077290490663	1.0	0.5910305340106511	77.35883475819348
GOTERM_BP_FAT	GO:0001525~angiogenesis	3	5.555555555555555	0.09008958641954389	7070,3553,1906	47	148	13528	5.834387579068429	1.0	0.592162612411822	77.76336483327114
GOTERM_BP_FAT	GO:0031644~regulation of neurological system process	3	5.555555555555555	0.09529642522101195	5021,6507,1906	47	153	13528	5.64372131831456	1.0	0.6105367713071908	79.70543759671737
GOTERM_BP_FAT	GO:0010647~positive regulation of cell communication	4	7.4074074074074066	0.10082378998136374	5021,3553,6507,5788	47	329	13528	3.4994503007178426	1.0	0.6259203037906597	81.59243443498934
GOTERM_BP_FAT	GO:0001932~regulation of protein amino acid phosphorylation	3	5.555555555555555	0.11693860543346996	3553,1906,5788	47	173	13528	4.9912679867175	1.0	0.6710763542464311	86.19851305638677
GOTERM_BP_FAT	GO:0051130~positive regulation of cellular component organization	3	5.555555555555555	0.12592070395528462	5021,3553,1906	47	181	13528	4.770659456917833	1.0	0.6967849714625384	88.272119058937
GOTERM_BP_FAT	GO:0044093~positive regulation of molecular function	5	9.25925925925926	0.13713989721578065	7070,800,3553,1906,5788	47	586	13528	2.455885556604459	1.0	0.7266626670525078	90.4528142113603
GOTERM_BP_FAT	GO:0045860~positive regulation of protein kinase activity	3	5.555555555555555	0.175410553210257	3553,1906,5788	47	223	13528	3.8721496040454153	1.0	0.796237644848153	95.3642628115751
GOTERM_BP_FAT	GO:0033674~positive regulation of kinase activity	3	5.555555555555555	0.1851805395380181	3553,1906,5788	47	231	13528	3.738049184857695	1.0	0.8104916232898012	96.16569233999334
GOTERM_BP_FAT	GO:0051347~positive regulation of transferase activity	3	5.555555555555555	0.19626733989240022	3553,1906,5788	47	240	13528	3.5978723404255315	1.0	0.8235759002846907	96.9172446319901
GOTERM_BP_FAT	GO:0045321~leukocyte activation	3	5.555555555555555	0.19874330147250457	7412,1906,5788	47	242	13528	3.568137858273255	1.0	0.8255872519997713	97.06504813259414
GOTERM_BP_FAT	GO:0010627~regulation of protein kinase cascade	3	5.555555555555555	0.20744023356368888	3553,1906,5788	47	249	13528	3.4678287618559342	1.0	0.8356234211509013	97.53325723129684
GOTERM_BP_FAT	GO:0007610~behavior	4	7.4074074074074066	0.21319907252721412	5021,3553,6507,4886	47	469	13528	2.454838270652815	1.0	0.8404564539566413	97.80371811096899
GOTERM_BP_FAT	GO:0016337~cell-cell adhesion	3	5.555555555555555	0.2413305500730002	7412,7070,5788	47	276	13528	3.128584643848288	1.0	0.8755872236571898	98.7700602895255
GOTERM_BP_FAT	GO:0043085~positive regulation of catalytic activity	4	7.4074074074074066	0.2594872265840371	7070,3553,1906,5788	47	520	13528	2.214075286415712	1.0	0.8947037409999836	99.16371133773812
GOTERM_BP_FAT	GO:0031399~regulation of protein modification process	3	5.555555555555555	0.2653688662880838	3553,1906,5788	47	295	13528	2.9270825820411104	1.0	0.8991952753555598	99.26344413033054
GOTERM_BP_FAT	GO:0007268~synaptic transmission	3	5.555555555555555	0.26916981874630375	5021,6507,4885	47	298	13528	2.8976153077252604	1.0	0.9014276615777878	99.32184364280538
GOTERM_BP_FAT	GO:0001501~skeletal system development	3	5.555555555555555	0.29576470110995157	1281,5156,1906	47	319	13528	2.706863202827986	1.0	0.9196077136305283	99.62419332337896
GOTERM_BP_FAT	GO:0051726~regulation of cell cycle	3	5.555555555555555	0.3109205115010065	3553,1906,5788	47	331	13528	2.6087291894324096	1.0	0.9274916854552742	99.73423285253959
GOTERM_BP_FAT	GO:0019226~transmission of nerve impulse	3	5.555555555555555	0.33479310962244646	5021,6507,4885	47	350	13528	2.467112462006079	1.0	0.9412784930535558	99.84841567184617
GOTERM_BP_FAT	GO:0050890~cognition	5	9.25925925925926	0.3737708651131038	157506,5021,3553,6507,4886	47	909	13528	1.5832221520024343	1.0	0.9597586773541595	99.94204970533409
GOTERM_BP_FAT	GO:0050877~neurological system process	6	11.11111111111111	0.39444697751485813	157506,5021,3553,6507,4885,4886	47	1210	13528	1.4272551433093017	1.0	0.9673287218882618	99.96604862523047
GOTERM_BP_FAT	GO:0006955~immune response	4	7.4074074074074066	0.41868757742574625	5553,3553,629,5788	47	690	13528	1.6685784767190872	1.0	0.974684449305478	99.98228611833927
GOTERM_BP_FAT	GO:0032268~regulation of cellular protein metabolic process	3	5.555555555555555	0.48269233601879213	3553,1906,5788	47	474	13528	1.8217075141395096	1.0	0.9861049920775404	99.99723584905692
GOTERM_BP_FAT	GO:0010604~positive regulation of macromolecule metabolic process	4	7.4074074074074066	0.5645413517906037	5156,7026,3553,5788	47	857	13528	1.3434295786886465	1.0	0.9951495698061555	99.99982202096282
GOTERM_BP_FAT	GO:0007166~cell surface receptor linked signal transduction	7	12.962962962962962	0.6180295911972736	1281,7070,5156,5021,4886,1906,5788	47	1856	13528	1.085564930300807	1.0	0.9978272802019885	99.99997792074731
GOTERM_BP_FAT	GO:0045935~positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	3	5.555555555555555	0.6331705617425778	5156,7026,5788	47	624	13528	1.38379705400982	1.0	0.9982557590507021	99.9999884052888
GOTERM_BP_FAT	GO:0007600~sensory perception	3	5.555555555555555	0.7709620164000096	157506,6507,4886	47	810	13528	1.0660362490149724	1.0	0.9998902617336282	99.99999999359123
GOTERM_BP_FAT	GO:0007186~G-protein coupled receptor protein signaling pathway	3	5.555555555555555	0.9045063279387571	5021,4886,1906	47	1123	13528	0.7689130558344859	1.0	0.9999994672187325	99.99999999999999

Annotation Cluster 6	Enrichment Score: 1.3592005006484587
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0006916~anti-apoptosis	5	9.25925925925926	0.005170190372642541	1410,673,4353,3553,5055	47	206	13528	6.986159884321421	0.9959754918954242	0.14579280920445825	7.923171490059122
GOTERM_BP_FAT	GO:0043066~negative regulation of apoptosis	5	9.25925925925926	0.0317607324369962	1410,673,4353,3553,5055	47	354	13528	4.065392475057099	0.9999999999999988	0.35981383260919675	40.18917836219692
GOTERM_BP_FAT	GO:0043069~negative regulation of programmed cell death	5	9.25925925925926	0.03319450335991771	1410,673,4353,3553,5055	47	359	13528	4.008771409944882	0.9999999999999998	0.3581737780872838	41.5841109334085
GOTERM_BP_FAT	GO:0060548~negative regulation of cell death	5	9.25925925925926	0.03348578335838204	1410,673,4353,3553,5055	47	360	13528	3.9976359338061465	0.9999999999999998	0.3572116759773474	41.86374838732833
GOTERM_BP_FAT	GO:0042981~regulation of apoptosis	7	12.962962962962962	0.053455290134839566	695,1410,673,4353,3553,5788,5055	47	804	13528	2.5059807346247482	1.0	0.4526181894299085	58.30761572108869
GOTERM_BP_FAT	GO:0043067~regulation of programmed cell death	7	12.962962962962962	0.05560223036539585	695,1410,673,4353,3553,5788,5055	47	812	13528	2.4812912692589877	1.0	0.45927246914856223	59.78832185477416
GOTERM_BP_FAT	GO:0010941~regulation of cell death	7	12.962962962962962	0.05642088656677141	695,1410,673,4353,3553,5788,5055	47	815	13528	2.4721576817647826	1.0	0.4609347777710142	60.339841024785066
GOTERM_BP_FAT	GO:0043933~macromolecular complex subunit organization	4	7.4074074074074066	0.4370684949859479	1410,5320,673,4353	47	710	13528	1.6215762661072821	1.0	0.9775696158413113	99.98938057775146

Annotation Cluster 7	Enrichment Score: 1.2786161186233802
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0007267~cell-cell signaling	7	12.962962962962962	0.015381673037560162	945,5021,3553,6507,4258,4885,1906	47	600	13528	3.3580141843971627	0.9999999312833909	0.24387383536774043	21.8742601134708
GOTERM_BP_FAT	GO:0046394~carboxylic acid biosynthetic process	3	5.555555555555555	0.09740338150425328	6507,4258,1906	47	155	13528	5.570899107755662	1.0	0.6157552993238813	80.44515583175867
GOTERM_BP_FAT	GO:0016053~organic acid biosynthetic process	3	5.555555555555555	0.09740338150425328	6507,4258,1906	47	155	13528	5.570899107755662	1.0	0.6157552993238813	80.44515583175867

Annotation Cluster 8	Enrichment Score: 1.0592068817572682
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0045429~positive regulation of nitric oxide biosynthetic process	3	5.555555555555555	0.002279687258581288	3553,3043,1906	47	21	13528	41.118541033434646	0.9118183372046201	0.12620429704814295	3.569204876290022
GOTERM_BP_FAT	GO:0045428~regulation of nitric oxide biosynthetic process	3	5.555555555555555	0.003761252522712781	3553,3043,1906	47	27	13528	31.98108747044917	0.9818578591757724	0.13800056189258525	5.824434062273998
GOTERM_BP_FAT	GO:0008284~positive regulation of cell proliferation	5	9.25925925925926	0.05147308759984519	7412,5156,3553,1906,5788	47	414	13528	3.476205159831432	1.0	0.4501785790747824	56.8952985069815
GOTERM_BP_FAT	GO:0051173~positive regulation of nitrogen compound metabolic process	6	11.11111111111111	0.06631433228738538	5156,7026,3553,3043,1906,5788	47	644	13528	2.68164398044139	1.0	0.5077675296841472	66.46815034657382
GOTERM_BP_FAT	GO:0031328~positive regulation of cellular biosynthetic process	5	9.25925925925926	0.20269297862294378	5156,7026,3553,3043,1906	47	685	13528	2.1009473520733035	1.0	0.8300328862725678	97.2871522981994
GOTERM_BP_FAT	GO:0009891~positive regulation of biosynthetic process	5	9.25925925925926	0.20980479252213843	5156,7026,3553,3043,1906	47	695	13528	2.0707178937700905	1.0	0.8372513719111562	97.64787934333825
GOTERM_BP_FAT	GO:0010604~positive regulation of macromolecule metabolic process	4	7.4074074074074066	0.5645413517906037	5156,7026,3553,5788	47	857	13528	1.3434295786886465	1.0	0.9951495698061555	99.99982202096282
GOTERM_BP_FAT	GO:0045935~positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	3	5.555555555555555	0.6331705617425778	5156,7026,5788	47	624	13528	1.38379705400982	1.0	0.9982557590507021	99.9999884052888
GOTERM_BP_FAT	GO:0010557~positive regulation of macromolecule biosynthetic process	3	5.555555555555555	0.6589797908233601	5156,7026,3553	47	654	13528	1.3203201249268006	1.0	0.9988559369379044	99.99999637169805

Annotation Cluster 9	Enrichment Score: 0.9547330463793282
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0007243~protein kinase cascade	8	14.814814814814813	2.3077972847647784E-4	695,1410,5999,673,5021,3553,1906,5788	47	370	13528	6.223346751006325	0.21774771032311646	0.04010335480012295	0.3668755973940119
GOTERM_BP_FAT	GO:0042981~regulation of apoptosis	7	12.962962962962962	0.053455290134839566	695,1410,673,4353,3553,5788,5055	47	804	13528	2.5059807346247482	1.0	0.4526181894299085	58.30761572108869
GOTERM_BP_FAT	GO:0043067~regulation of programmed cell death	7	12.962962962962962	0.05560223036539585	695,1410,673,4353,3553,5788,5055	47	812	13528	2.4812912692589877	1.0	0.45927246914856223	59.78832185477416
GOTERM_BP_FAT	GO:0010941~regulation of cell death	7	12.962962962962962	0.05642088656677141	695,1410,673,4353,3553,5788,5055	47	815	13528	2.4721576817647826	1.0	0.4609347777710142	60.339841024785066
GOTERM_BP_FAT	GO:0006468~protein amino acid phosphorylation	5	9.25925925925926	0.19009277110129058	695,5156,673,3553,5788	47	667	13528	2.157644581964337	1.0	0.8172182524305142	96.5176930567707
GOTERM_BP_FAT	GO:0016310~phosphorylation	5	9.25925925925926	0.2882649969226607	695,5156,673,3553,5788	47	800	13528	1.798936170212766	1.0	0.9146770287191174	99.55513704592889
GOTERM_BP_FAT	GO:0006796~phosphate metabolic process	5	9.25925925925926	0.4241356409666739	695,5156,673,3553,5788	47	973	13528	1.4790842098357786	1.0	0.9756805497047776	99.98475274851013
GOTERM_BP_FAT	GO:0006793~phosphorus metabolic process	5	9.25925925925926	0.4241356409666739	695,5156,673,3553,5788	47	973	13528	1.4790842098357786	1.0	0.9756805497047776	99.98475274851013
GOTERM_BP_FAT	GO:0043065~positive regulation of apoptosis	3	5.555555555555555	0.4322058394584751	695,3553,5788	47	430	13528	2.0081147946561106	1.0	0.9773489188841976	99.98782174217826
GOTERM_BP_FAT	GO:0043068~positive regulation of programmed cell death	3	5.555555555555555	0.4357277805855829	695,3553,5788	47	433	13528	1.9942017591273156	1.0	0.9777464320927582	99.98897057589737
GOTERM_BP_FAT	GO:0010942~positive regulation of cell death	3	5.555555555555555	0.4380695755436831	695,3553,5788	47	435	13528	1.98503301540719	1.0	0.9773045034531666	99.98967735414037

Annotation Cluster 10	Enrichment Score: 0.8973591997304606
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0007584~response to nutrient	3	5.555555555555555	0.08194766537142452	3553,2029,629	47	140	13528	6.167781155015198	1.0	0.5726766805937503	74.37414981263693
GOTERM_BP_FAT	GO:0031667~response to nutrient levels	3	5.555555555555555	0.14435731040907573	3553,2029,629	47	197	13528	4.383194729452424	1.0	0.7375627435910969	91.64813879391835
GOTERM_BP_FAT	GO:0009991~response to extracellular stimulus	3	5.555555555555555	0.17176988842154983	3553,2029,629	47	220	13528	3.92495164410058	1.0	0.791248156409674	95.02736625283714

Annotation Cluster 11	Enrichment Score: 0.8482026879872226
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0007423~sensory organ development	4	7.4074074074074066	0.04266218472677767	1410,7070,5156,1906	47	229	13528	5.027594536839171	1.0	0.4027601838380097	50.05743635498081
GOTERM_BP_FAT	GO:0030334~regulation of cell migration	3	5.555555555555555	0.11251322839878178	7070,5156,1906	47	169	13528	5.10940450711318	1.0	0.6591381602658934	85.05492662525154
GOTERM_BP_FAT	GO:0040012~regulation of locomotion	3	5.555555555555555	0.13853319426209318	7070,5156,1906	47	192	13528	4.497340425531914	1.0	0.727607463761718	90.69537590657642
GOTERM_BP_FAT	GO:0051270~regulation of cell motion	3	5.555555555555555	0.1396936818912761	7070,5156,1906	47	193	13528	4.47403814353434	1.0	0.7279035608553106	90.89298609733099
GOTERM_BP_FAT	GO:0007166~cell surface receptor linked signal transduction	7	12.962962962962962	0.6180295911972736	1281,7070,5156,5021,4886,1906,5788	47	1856	13528	1.085564930300807	1.0	0.9978272802019885	99.99997792074731

Annotation Cluster 12	Enrichment Score: 0.5954378608875407
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0006928~cell motion	4	7.4074074074074066	0.21854655019594957	7412,7026,800,3553	47	475	13528	2.4238297872340424	1.0	0.8465158063533929	98.0297408818388
GOTERM_BP_FAT	GO:0016477~cell migration	3	5.555555555555555	0.2413305500730002	7412,7026,3553	47	276	13528	3.128584643848288	1.0	0.8755872236571898	98.7700602895255
GOTERM_BP_FAT	GO:0051674~localization of cell	3	5.555555555555555	0.2805731765439311	7412,7026,3553	47	307	13528	2.8126689306258226	1.0	0.9092669416265806	99.47208118499654
GOTERM_BP_FAT	GO:0048870~cell motility	3	5.555555555555555	0.2805731765439311	7412,7026,3553	47	307	13528	2.8126689306258226	1.0	0.9092669416265806	99.47208118499654

Annotation Cluster 13	Enrichment Score: 0.0171267008580914
Category	Term	Count	%	PValue	Genes	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GOTERM_BP_FAT	GO:0006355~regulation of transcription, DNA-dependent	4	7.4074074074074066	0.9511112533691608	5151,2625,7026,7738	47	1773	13528	0.6493621821410999	1.0	0.9999999903486564	100.0
GOTERM_BP_FAT	GO:0051252~regulation of RNA metabolic process	4	7.4074074074074066	0.95632712085812	5151,2625,7026,7738	47	1813	13528	0.6350353827557476	1.0	0.9999999945988295	100.0
GOTERM_BP_FAT	GO:0045449~regulation of transcription	6	11.11111111111111	0.9569067645070283	5151,2625,7026,3553,55885,7738	47	2601	13528	0.66396721391936	1.0	0.9999999944488585	100.0
GOTERM_BP_FAT	GO:0006350~transcription	4	7.4074074074074066	0.9812638043304253	2625,7026,55885,7738	47	2101	13528	0.5479862679372538	1.0	0.999999999958641	100.0

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