1 Design of the experiment

3 biological replicates, each one composed of a pair of MEFs clones coming from the same litter
For each biological replicate, each pair of clones is composed of:

an OsTIR1-only clone, which expresses OsTIR1 but not the AID-Ogt isoform, thus auxin treatment is not supposed to cause any OGT depletion. This clone represents the control of the corresponding biological replicate
an AID-Ogt;OsTIR clone, which bears both genomic modifications necessary to obtain OGT depletion after auxin treatment.

All clones (both controls and AID-Ogt;OsTIR clones) were collected in the following conditions:

without any auxin addition (No auxin)
after 24h of auxin treatment
after 48h of auxin treatment
after 4 days of auxin treatment.

2 PCA

The main factor separating the samples is the cell clone and clone’s litter (biological replicate) on PC1, then the condition dominates ordering along PC2 inside each clone’s cluster.

3 Plotting counts for Ogt, Oga, OsTIR

4 Diff Expr Analysis

4.1 P-value histograms and MA-plots for the different comparisons

The threshold used for a dot to be colored in blue in the MA-plots is: p-value adjusted < 0.05.

4.2 Volcano plots for the different comparisons

library(EnhancedVolcano)

volcano_plot <- function (i, my_res_list) {
  res_names <- retrieve_res_names(my_res_list[[i]])
  EnhancedVolcano(my_res_list[[i]], lab = res_names$gene_name, x = 'log2FoldChange', y = 'pvalue', xlim = c(-3,3), ylim = c(0,60),
                  FCcutoff = 0.3,
                  title = names(my_res_list)[i],
                  labSize = 3,
                  max.overlaps = 30,
                  drawConnectors = TRUE)
}

lapply(1:7, volcano_plot, my_res_list = my_res_list)

4.3 Getting DE genes, ordered by p-value

Getting the DE genes (padj < 0.05, any log2FC), ordered by pvalue.

4.4 DE genes over-representation tests

I use the DE genes observed in AID cells after 24h/48h/4d of auxin treatment (compared to the NO auxin condition), after exclusion of the DE genes observed by treating ctrl cells with auxin at any of the three time points.

4.4.1 Overlap between groups of DEGs

Overlap of DEGs due to OGT depletion with DEGs due to auxin effect on ctrl cells:

Overlap of DEGs at different time points of OGT depletion (auxin effect’s DEGs were excluded):

Pvalues of overlaps for upregulated DEGs are:

6.1496325^{-166} for AID-Ogt 24h aux & AID-Ogt 48h aux, both w/o auxin-effect genes
4.5697982^{-172} for AID-Ogt 24h aux & AID-Ogt 4d aux, both w/o auxin-effect genes
1.3717679^{-244} for AID-Ogt 48h aux & AID-Ogt 4d aux, both w/o auxin-effect genes
6.9704315^{-13} for AID-Ogt 4d aux & 4d aux on ctrl cells

Pvalues of overlaps for downregulated DEGs are:

7.3400989^{-224} for AID-Ogt 24h aux & AID-Ogt 48h aux, both w/o auxin-effect genes
1.9600784^{-281} for AID-Ogt 24h aux & AID-Ogt 4d aux, both w/o auxin-effect genes
0 for AID-Ogt 48h aux & AID-Ogt 4d aux, both w/o auxin-effect genes
0.9786367 for AID-Ogt 4d aux & 4d aux on ctrl cells

Note that:

pval decreases for with longer treatment –> effects at 48h and 4d time points are more similar between each other than to the 24h time point
the pval is much higher when comparing 4d-treated AID-Ogt cells and 4d-treated control cells.

4.4.2 Gene Ontology Over-representation Test - up and downregulated genes separately

genotype effect - BP up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

genotype effect - CC up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

genotype effect - MF up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

24h auxin on AID-Ogt cells - BP up
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0022613	GO:0022613	ribonucleoprotein complex biogenesis	22/472	411/22853	0.0000514	0.0208542	0.0199494	Mrps7/Rrp15/Las1l/Gemin6/Ddx17/Bms1/LTO1/Gemin4/Frg1/Bysl/Emg1/Ddx51/Zfp622/Nvl/Npm3/Rpusd3/Rpusd1/Snu13/Xab2/Ncbp1/Exosc5/Crnkl1	22
GO:0044270	GO:0044270	cellular nitrogen compound catabolic process	21/472	412/22853	0.0001499	0.0395218	0.0378071	Nudt19/Nudt9/Nit1/Rida/Apex1/E2f1/Phax/Dctpp1/Zfp36l2/Fastkd1/Vim/Hmox1/Rnaseh2a/Pde12/Entpd5/Hint1/Smg8/Tymp/Ncbp1/Rbm8a/Exosc5	21
GO:0051099	GO:0051099	positive regulation of binding	13/472	194/22853	0.0002098	0.0465691	0.0445487	Ngf/Nme1/Ripor2/Ramp1/Eif2b4/Anxa2/Eif2b1/S100a10/Psen1/Nvl/Smarca4/Ncbp1/Pparg	13

24h auxin on AID-Ogt cells - CC up
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0098798	GO:0098798	mitochondrial protein-containing complex	22/486	260/22838	0.00e+00	0.0000210	0.0000182	Tomm22/Bckdha/Mrpl34/Mrps7/Mrpl42/Chchd6/Ndufb10/Mrps21/Mrps6/Uqcc3/Mrpl33/Mrpl45/Cox5a/Mrpl35/Chchd3/Mrpl38/Mrpl28/Mrpl17/Ndufb9/Mrps22/Ndufs7/Micos13	22
GO:1905369	GO:1905369	endopeptidase complex	10/486	70/22838	2.20e-06	0.0001674	0.0001453	Htra2/Psmb7/Psmb1/Psmd4/Psma7/Psmb5/Psma4/Psmc2/Hspb1/Ecpas	10
GO:0000315	GO:0000315	organellar large ribosomal subunit	8/486	58/22838	2.99e-05	0.0015193	0.0013193	Mrpl34/Mrpl42/Mrpl33/Mrpl45/Mrpl35/Mrpl38/Mrpl28/Mrpl17	8
GO:0005839	GO:0005839	proteasome core complex	5/486	19/22838	3.88e-05	0.0017750	0.0015413	Psmb7/Psmb1/Psma7/Psmb5/Psma4	5
GO:0098573	GO:0098573	intrinsic component of mitochondrial membrane	9/486	81/22838	5.58e-05	0.0019612	0.0017030	Chchd6/Slc25a19/Synj2bp/Uqcc3/Coa3/Cox18/Adck1/Chchd3/Micos13	9

24h auxin on AID-Ogt cells - MF up
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0003906	GO:0003906	DNA-(apurinic or apyrimidinic site) endonuclease activity	4/472	13/22360	0.0001205	0.0403050	0.0356067	Hmga1b/Apex1/Nthl1/Hmga2	4
GO:0070003	GO:0070003	threonine-type peptidase activity	4/472	19/22360	0.0005907	0.0429728	0.0379635	Psmb7/Psmb1/Psmb5/Psma4	4

48h auxin on AID-Ogt cells - BP up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

48h auxin on AID-Ogt cells - CC up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

48h auxin on AID-Ogt cells - MF up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

4d auxin on AID-Ogt cells - BP up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

4d auxin on AID-Ogt cells - CC up
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0005774	GO:0005774	vacuolar membrane	13/410	226/22838	0.0002405	0.0359122	0.0328239	Pld3/Mcoln1/Abcd4/Vps13a/Npc1/Cyb561a3/Atg16l2/Stx8/Slc48a1/Nprl2/Gpr137b/Vamp8/H2-M3	13

4d auxin on AID-Ogt cells - MF up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

4d auxin on ctrl cells - BP up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

4d auxin on ctrl cells - CC up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

4d auxin on ctrl cells - MF up
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

genotype effect - BP down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0007015	GO:0007015	actin filament organization	25/189	456/22853	0.0000000	0.0000000	0.0000000	Fscn1/Pfn1/Cdc42ep3/Dpysl3/Cfl1/Mical2/Arpc5/Cfl2/Actg1/Fermt2/Tmsb4x/Acta1/Cdc42ep1/Srf/Tnfaip1/Tnnt2/Arhgef5/Vasp/Sorbs2/Capzb/Myo1c/Arpc4/Tmsb10/Pawr/Swap70	25
GO:0032970	GO:0032970	regulation of actin filament-based process	22/189	417/22853	0.0000000	0.0000000	0.0000000	Fscn1/Pfn1/Cdc42ep3/Sema3e/Cfl1/Arpc5/Cfl2/Epha3/Actg1/Fermt2/Tmsb4x/Cdc42ep1/Tnnt2/Ilk/Arhgef5/Vasp/Capzb/Myo1c/Arpc4/Tmsb10/Cnn2/Swap70	22
GO:0032535	GO:0032535	regulation of cellular component size	20/189	417/22853	0.0000000	0.0000002	0.0000002	Pfn1/Cdc42ep3/Sema3e/Cfl1/Arpc5/Cfl2/Ngf/Rab3b/Tmsb4x/Cdc42ep1/Srf/Ilk/Vasp/Capzb/Myo1c/Chmp3/Akt1/Arpc4/Tmsb10/Swap70	20
GO:0042692	GO:0042692	muscle cell differentiation	18/189	426/22853	0.0000000	0.0000059	0.0000048	Pdlim5/Cfl2/Actg1/Csrp1/Tmsb4x/Acta1/Tbx2/Hacd1/Srf/Tnnt2/Igf2/Fhl2/Hdac5/Sorbs2/Capzb/Mapk14/Homer1/Akt1	18
GO:1902903	GO:1902903	regulation of supramolecular fiber organization	16/189	389/22853	0.0000002	0.0000407	0.0000334	Pfn1/Cdc42ep3/Cfl1/Arpc5/Cfl2/Actg1/Fermt2/Tmsb4x/Cdc42ep1/Arhgef5/Vasp/Capzb/Myo1c/Arpc4/Tmsb10/Swap70	16
GO:0010810	GO:0010810	regulation of cell-substrate adhesion	12/189	226/22853	0.0000004	0.0000664	0.0000545	Sema3e/Cfl1/Spry4/Epha3/Actg1/Fermt2/Hacd1/Peak1/Ilk/Rras/Itga5/Itga3	12
GO:0043254	GO:0043254	regulation of protein-containing complex assembly	16/189	452/22853	0.0000012	0.0001705	0.0001400	Fscn1/Pfn1/Cdc42ep3/Cfl1/Arpc5/Fblim1/Fermt2/Tmsb4x/Cdc42ep1/Arhgef5/Vasp/Capzb/Myo1c/Raf1/Arpc4/Tmsb10	16
GO:0007264	GO:0007264	small GTPase mediated signal transduction	15/189	425/22853	0.0000027	0.0003517	0.0002887	Cdc42ep3/Spry4/Rassf1/Ngf/Ppp2cb/Ywhaq/F2r/Cdc42ep1/Rasgrp2/Tnfaip1/Adcyap1r1/Garre1/Rras/Itga3/Dock8	15
GO:0001667	GO:0001667	ameboidal-type cell migration	15/189	442/22853	0.0000044	0.0005211	0.0004278	Alx1/Pfn1/Sema3e/Cfl1/Clec14a/Srf/Igf2/Ilk/Hdac5/Gpi1/Cap1/Rras/Gdf6/Akt1/Itga3	15
GO:0060562	GO:0060562	epithelial tube morphogenesis	14/189	391/22853	0.0000051	0.0005730	0.0004704	Alx1/Fat4/Pfn1/Flt1/Sema3e/Cfl1/Hmga2/Foxd1/Tbx2/Srf/Ilk/Hdac5/Vasp/Ppp1ca	14
GO:0060537	GO:0060537	muscle tissue development	15/189	482/22853	0.0000124	0.0013049	0.0010711	Ybx3/Pdlim5/Zfpm1/Cfl2/Csrp1/Acta1/Tbx2/Srf/Tnnt2/Igf2/Fhl2/Hdac5/Sorbs2/Mapk14/Homer1	15
GO:0045927	GO:0045927	positive regulation of growth	12/189	320/22853	0.0000154	0.0015133	0.0012422	Ybx3/Cfl1/Ngf/Hmga2/Rftn1/Tbx2/Srf/Igf2/Ilk/Avpr1a/Mapk14/Akt1	12
GO:0090398	GO:0090398	cellular senescence	6/189	67/22853	0.0000194	0.0017098	0.0014035	Hmga2/Hmga1b/Tbx2/Srf/Mapk14/Pawr	6
GO:0030239	GO:0030239	myofibril assembly	6/189	69/22853	0.0000230	0.0018792	0.0015425	Cfl2/Actg1/Csrp1/Acta1/Srf/Tnnt2	6
GO:0060485	GO:0060485	mesenchyme development	11/189	292/22853	0.0000337	0.0026078	0.0021406	Alx1/Sema3e/Cfl1/Tgfb1i1/Epha3/Pax1/Hmga2/Fermt2/Foxd1/Tbx2/Pawr	11
GO:0002040	GO:0002040	sprouting angiogenesis	7/189	123/22853	0.0000750	0.0045022	0.0036957	Flt1/Sema3e/Clec14a/Srf/Hdac5/Akt1/Itga5	7
GO:0001649	GO:0001649	osteoblast differentiation	9/189	220/22853	0.0000944	0.0053421	0.0043851	Fermt2/Cebpa/Igf2/Ilk/Fhl2/Hdac5/Mapk14/Akt1/Pdlim7	9
GO:0007160	GO:0007160	cell-matrix adhesion	9/189	225/22853	0.0001120	0.0061020	0.0050088	Sema3e/Cfl1/Epha3/Actg1/Fermt2/Srf/Peak1/Ilk/Rras	9
GO:0042989	GO:0042989	sequestering of actin monomers	3/189	12/22853	0.0001159	0.0062035	0.0050922	Pfn1/Tmsb4x/Tmsb10	3
GO:2000648	GO:2000648	positive regulation of stem cell proliferation	4/189	31/22853	0.0001197	0.0062632	0.0051412	Ngf/Hmga2/Fermt2/Hdac5	4
GO:0022604	GO:0022604	regulation of cell morphogenesis	11/189	337/22853	0.0001213	0.0062632	0.0051412	Cdc42ep3/Aldoa/Sema3e/Cfl1/Myl12a/Spry4/Fblim1/Fermt2/Cdc42ep1/Ilk/Capzb	11
GO:2000774	GO:2000774	positive regulation of cellular senescence	3/189	13/22853	0.0001498	0.0069977	0.0057441	Hmga2/Hmga1b/Pawr	3
GO:0043243	GO:0043243	positive regulation of protein-containing complex disassembly	4/189	35/22853	0.0001942	0.0081627	0.0067004	Oga/Cfl1/Cfl2/Nes	4
GO:0043954	GO:0043954	cellular component maintenance	5/189	68/22853	0.0002508	0.0095863	0.0078690	Cfl1/F2r/Fermt2/Homer1/Itga3	5
GO:0032507	GO:0032507	maintenance of protein location in cell	5/189	69/22853	0.0002686	0.0097596	0.0080112	Pfn1/Txn1/Tmsb4x/Akt1/Tmsb10	5
GO:0006936	GO:0006936	muscle contraction	10/189	312/22853	0.0002855	0.0102178	0.0083873	Aldoa/Flt1/F2r/Tbx2/Srf/Eno1b/Tnnt2/Cacnb2/Homer1/Pawr	10
GO:0034446	GO:0034446	substrate adhesion-dependent cell spreading	6/189	109/22853	0.0002956	0.0102909	0.0084474	Spry4/Fermt2/Peak1/Ilk/Axl/Mertk	6
GO:0045444	GO:0045444	fat cell differentiation	9/189	258/22853	0.0003106	0.0105058	0.0086237	Zfpm1/Tgfb1i1/Hmga2/Fermt2/Cebpa/Mapk14/Tbl1x/Gdf6/Akt1	9
GO:0042220	GO:0042220	response to cocaine	4/189	43/22853	0.0004346	0.0133237	0.0109368	Htr1b/Tgm2/Hdac5/Homer1	4
GO:1902414	GO:1902414	protein localization to cell junction	6/189	119/22853	0.0004732	0.0143557	0.0117840	Actb/Actg1/Fermt2/Nptx2/Lamtor3/Homer1	6
GO:0090100	GO:0090100	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	6/189	120/22853	0.0004947	0.0147057	0.0120713	Tgfb1i1/Foxd1/Inhba/Rbpms/Ilk/Gdf6	6
GO:0032881	GO:0032881	regulation of polysaccharide metabolic process	4/189	46/22853	0.0005637	0.0159990	0.0131329	Igf2/Ap2a1/Akt1/Ppp1ca	4
GO:0045933	GO:0045933	positive regulation of muscle contraction	4/189	51/22853	0.0008359	0.0210272	0.0172604	F2r/Srf/Eno1b/Pawr	4
GO:0048872	GO:0048872	homeostasis of number of cells	10/189	360/22853	0.0008672	0.0215850	0.0177183	Zfpm1/F2r/Inhba/Srf/Arhgef5/Gpi1/Axl/Mertk/Mapk14/Akt1	10
GO:0051402	GO:0051402	neuron apoptotic process	9/189	308/22853	0.0011015	0.0257467	0.0211344	Ngf/F2r/Egln3/Ilk/Atn1/Gpi1/Nes/Axl/Pawr	9
GO:0048538	GO:0048538	thymus development	4/189	56/22853	0.0011898	0.0265275	0.0217753	Pax1/Srf/Raf1/Hoxa3	4
GO:0032878	GO:0032878	regulation of establishment or maintenance of cell polarity	3/189	26/22853	0.0012582	0.0274980	0.0225720	Cfl1/Dock8/Llgl2	3
GO:0016051	GO:0016051	carbohydrate biosynthetic process	7/189	198/22853	0.0013373	0.0285185	0.0234097	Chst12/Igf2/Ap2a1/Gpi1/Adcyap1r1/Akt1/Ppp1ca	7
GO:0001704	GO:0001704	formation of primary germ layer	5/189	102/22853	0.0015989	0.0329055	0.0270108	Hmga2/Inhba/Srf/Gpi1/Itga5	5
GO:0043270	GO:0043270	positive regulation of ion transport	9/189	328/22853	0.0016989	0.0340125	0.0279195	Oga/Cfl1/Rab3b/F2r/Avpr1a/Adcyap1r1/Cacnb2/Homer1/Akt1	9
GO:0071456	GO:0071456	cellular response to hypoxia	5/189	105/22853	0.0018171	0.0350210	0.0287473	Eno1b/Gnb1/Egln3/Ubqln1/Akt1	5
GO:0010634	GO:0010634	positive regulation of epithelial cell migration	6/189	156/22853	0.0019269	0.0361210	0.0296503	Pfn1/Igf2/Gpi1/Rras/Akt1/Itga3	6
GO:0098742	GO:0098742	cell-cell adhesion via plasma-membrane adhesion molecules	7/189	213/22853	0.0020266	0.0372770	0.0305992	Fat4/Scarf2/Palld/Epha3/Mcam/Mapk14/Itga5	7
GO:0040013	GO:0040013	negative regulation of locomotion	9/189	341/22853	0.0022101	0.0391820	0.0321629	Dpysl3/Sema3e/Cfl1/Srf/Ilk/Hdac5/Rras/Akt1/Cnn2	9
GO:0048608	GO:0048608	reproductive structure development	11/189	481/22853	0.0022961	0.0404473	0.0332015	Ybx3/Hmga2/Inhba/Cebpa/Igf2/Atn1/Axl/Mertk/Mapk14/Akt1/Llgl2	11
GO:0043393	GO:0043393	regulation of protein binding	7/189	218/22853	0.0023089	0.0404473	0.0332015	Actb/Zfpm1/Ngf/Ppp2cb/Hdac5/Nes/Akt1	7
GO:0061621	GO:0061621	canonical glycolysis	2/189	10/22853	0.0029309	0.0472847	0.0388141	Eno1b/Gpi1	2

genotype effect - CC down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0001725	GO:0001725	stress fiber	12/192	88/22838	0.0000000	0.0000000	0.0000000	Fscn1/Actb/Pdlim5/Fhl3/Myl12a/Palld/Fblim1/Fermt2/Acta1/Ilk/Pdlim7/Cnn2	12
GO:0030016	GO:0030016	myofibril	16/192	222/22838	0.0000000	0.0000000	0.0000000	Aldoa/Pdlim5/Fhl3/Myl12a/Palld/Cfl2/Actg1/Csrp1/Acta1/Tnnt2/Ilk/Fhl2/Cab39/Capzb/Homer1/Pdlim7	16
GO:0030055	GO:0030055	cell-substrate junction	10/192	180/22838	0.0000031	0.0000728	0.0000601	Cfl1/Palld/Fblim1/Tgfb1i1/Fermt2/Peak1/Ilk/Vasp/Itga5/Pdlim7	10
GO:0030027	GO:0030027	lamellipodium	9/192	174/22838	0.0000172	0.0003516	0.0002903	Fscn1/Actb/Dpysl3/Cfl1/Palld/Arpc5/Ilk/Vasp/Capzb	9
GO:0009898	GO:0009898	cytoplasmic side of plasma membrane	9/192	177/22838	0.0000197	0.0003776	0.0003118	Gnb2/Fermt2/Snx18/Gnb1/Traf5/Esyt1/Litaf/S100a6/Gnai3	9
GO:0045121	GO:0045121	membrane raft	11/192	393/22838	0.0005193	0.0064912	0.0053591	Prkar2b/Actb/Rftn1/F2r/Eno1b/Serpinh1/Plpp2/Adcyap1r1/Lamtor3/Myo1c/Gnai3	11
GO:1905369	GO:1905369	endopeptidase complex	4/192	70/22838	0.0028805	0.0285218	0.0235474	Psmd3/Ubqln1/Ubr1/Psma7	4
GO:0030863	GO:0030863	cortical cytoskeleton	5/192	123/22838	0.0038706	0.0370124	0.0305572	Actb/Cfl1/Cap1/Capzb/Llgl2	5

genotype effect - MF down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0003779	GO:0003779	actin binding	24/189	444/22360	0.00e+00	0.0000000	0.0000000	Fscn1/Pfn1/Pdlim5/Fhl3/Cfl1/Mical2/Palld/Arpc5/Cfl2/Fermt2/Ppp1r18/Tmsb4x/Tnnt2/Tagln/Cap1/Vasp/Capzb/Myo1c/Cacnb2/Arpc4/Pdlim7/Tmsb10/Cnn2/Pawr	24
GO:0051020	GO:0051020	GTPase binding	12/189	313/22360	1.53e-05	0.0017714	0.0014927	Pfn1/Rassf1/Sh3gl1/Gnb2/Tnfaip1/Eno1b/Gnb1/Adcyap1r1/Myo1c/Garre1/Rassf5/Raf1	12

24h auxin on AID-Ogt cells - BP down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0006888	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	21/595	116/22853	0.0000000	0.0000000	0.0000000	Copb2/Kdelr2/Sec24d/Sec24a/Scfd1/Copg1/Sec31a/Rab1a/Tmed10/Copa/Lman1/Sar1a/Arf1/Sec23a/Yipf5/Golga2/Copb1/Kdelr3/Creb3l2/Tmed9/Uso1	21
GO:0006890	GO:0006890	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	13/595	45/22853	0.0000000	0.0000001	0.0000001	Copb2/Kdelr2/Scfd1/Copa/Copz2/Copz1/Rab6a/Kdelr3/Golph3/Atp9a/Nbas/Gbf1/Kif1c	13
GO:0048660	GO:0048660	regulation of smooth muscle cell proliferation	20/595	178/22853	0.0000000	0.0000247	0.0000205	Adamts1/Vip/Ndrg4/Rhoa/Hmgcr/Rgs5/Shc1/Cnn1/Htr1b/Pdgfd/Npr3/Gnai3/Prkg1/Ereg/Hif1a/Klf4/Tgfb3/Ogn/Zfp143/Sf1	20
GO:0009100	GO:0009100	glycoprotein metabolic process	28/595	331/22853	0.0000001	0.0000247	0.0000205	Oga/Rxylt1/Gmppb/Tmem59/Fam20b/Rab1a/Bpnt2/Ostc/Magt1/Dsel/Alg14/Pofut2/Man1c1/Pgm3/Pomt2/Itm2a/Tmem258/Slc2a10/Hs6st2/Golph3/Ganab/Stt3a/Hif1a/Fbxo44/Rpn1/Galnt11/Gxylt1/Csgalnact2	28
GO:0010256	GO:0010256	endomembrane system organization	33/595	486/22853	0.0000006	0.0001843	0.0001532	Arl1/Ndel1/Esyt1/Sec31a/Rab1a/Tmed10/Rab5a/Lman1/Emc2/Yipf5/Osbp/Fat4/Plscr3/Ccdc136/Prx/Cltc/Lysmd3/Golga2/Rab18/Eif2ak3/Map2k2/Nup93/Tmed9/Mapk1/Atp8b2/Vti1b/Golph3/Golga5/Sec23ip/Arfgef2/Gbf1/Parp11/Uso1	33
GO:1904951	GO:1904951	positive regulation of establishment of protein localization	26/595	333/22853	0.0000007	0.0002002	0.0001664	Oga/Ppp3cb/Sec24a/Tcaf1/Tmed10/Pmaip1/Sar1a/Tcp1/Bbc3/Arf1/Tm7sf3/Osbp/Kif5b/Fis1/Tcaf2/Mapk1/Vamp2/Ipo5/Golph3/Vps35/Hif1a/Stom/Tgfb3/Gli3/Ppia/Pfkfb2	26
GO:0090150	GO:0090150	establishment of protein localization to membrane	22/595	254/22853	0.0000010	0.0002245	0.0001866	Oga/Hspa5/Tcaf1/Clstn1/Pmaip1/Emc2/Bbc3/Fis1/Tcaf2/Ssr3/Hspa4/Vamp2/Timm13/Golph3/Vps35/Srpr/Golga4/Stom/Tamalin/Calm3/Tomm40/Gga2	22
GO:0051222	GO:0051222	positive regulation of protein transport	25/595	317/22853	0.0000010	0.0002260	0.0001879	Oga/Ppp3cb/Sec24a/Tcaf1/Tmed10/Pmaip1/Sar1a/Bbc3/Arf1/Tm7sf3/Osbp/Kif5b/Fis1/Tcaf2/Mapk1/Vamp2/Ipo5/Golph3/Vps35/Hif1a/Stom/Tgfb3/Gli3/Ppia/Pfkfb2	25
GO:0090287	GO:0090287	regulation of cellular response to growth factor stimulus	24/595	300/22853	0.0000013	0.0002745	0.0002282	Spry1/Fbn2/Hspa5/Jcad/Tob1/Cyfip2/Got1/Aspn/Slc2a10/Spry2/Fbn1/Glg1/Fzd4/Spred3/Hif1a/Chrd/Hes1/Vegfd/Tgfb3/Lats1/Fstl1/Grem1/Ccn1/Slit2	24
GO:0006986	GO:0006986	response to unfolded protein	14/595	118/22853	0.0000025	0.0004048	0.0003365	Hspa9/Hspa5/Selenos/Dnajc3/Tm7sf3/Eif2ak2/Eif2ak3/Manf/Creb3l2/Ddit3/Atf4/Derl1/Tbl2/Hspb8	14
GO:0034976	GO:0034976	response to endoplasmic reticulum stress	21/595	255/22853	0.0000038	0.0005397	0.0004487	Hspa5/Selenos/Ufm1/Pmaip1/Dnajc3/Bbc3/Canx/Eif2ak2/Eif2ak3/Tmem259/Sesn2/Usp25/Manf/Creb3l2/Ddit3/Pdia3/Atf4/Derl1/Nfe2l1/Tbl2/Fbxo44	21
GO:0090092	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	21/595	255/22853	0.0000038	0.0005397	0.0004487	Tgfbr1/Spry1/Fbn2/Hspa5/Tob1/Got1/Aspn/Nup93/Slc2a10/Spry2/Fbn1/Glg1/Spred3/Chrd/Hes1/Tgfb3/Lats1/Fstl1/Gdf11/Grem1/Ccn1	21
GO:0071692	GO:0071692	protein localization to extracellular region	27/595	402/22853	0.0000079	0.0010224	0.0008500	Oga/Ppp3cb/Sec24a/Fbn2/Cyp51/Copg1/Tmed10/Arf1/Ccdc186/Tm7sf3/Pfkl/Osbp/Hmgcr/Kif5b/Cdk16/Midn/Hmgn3/Fbn1/Ppp3ca/Golph3/Vps35/Rab11fip1/Hif1a/Tgfb3/Ppia/Pfkfb2/Arfip1	27
GO:0035150	GO:0035150	regulation of tube size	16/595	172/22853	0.0000117	0.0012454	0.0010354	Rhoa/Atp2b1/Icam1/Hmgcr/Shc1/Manf/Ahr/Htr1b/Ece1/Npr3/Prkg1/Cacna1g/Htr2a/Hif1a/Sod3/Ptprm	16
GO:1901998	GO:1901998	toxin transport	8/595	43/22853	0.0000131	0.0013554	0.0011269	Copb2/Hspa5/Scfd1/Tcp1/Bbc3/Copz1/Nrp1/Mtmr12	8
GO:0003018	GO:0003018	vascular process in circulatory system	19/595	235/22853	0.0000140	0.0014182	0.0011791	Rhoa/Atp2b1/Icam1/Hmgcr/Amot/Shc1/Manf/Abcg2/Ahr/Htr1b/Ece1/Npr3/Prkg1/Cacna1g/Htr2a/Hif1a/Sod3/Ptprm/Slit2	19
GO:0034248	GO:0034248	regulation of cellular amide metabolic process	28/595	446/22853	0.0000188	0.0018187	0.0015120	Eif5a2/Abce1/Tmed10/Tob1/Dnajc3/Stat3/Ireb2/Eif2s3y/Eif2ak2/Eif2ak3/Sesn2/Cpeb4/Aars/Mapk1/Paip2b/Polr2g/Zfp36l1/Ago3/Cyp1b1/Eif5/Btg2/Fto/Sp1/Eif2s3x/Secisbp2l/Ncl/Npm1/Ccn1	28
GO:0002040	GO:0002040	sprouting angiogenesis	13/595	123/22853	0.0000199	0.0018843	0.0015666	Jcad/Rhoa/Adamts9/Ephb4/Reck/Nrp1/Plk2/Vegfd/Klf4/Akt3/Grem1/Slit2/Nr4a1	13
GO:0048880	GO:0048880	sensory system development	26/595	427/22853	0.0000615	0.0041571	0.0034562	Tgfbr1/Spry1/Lif/Cc2d2a/Stat3/Col5a2/Hdac2/Ahr/Spry2/Nhs/Nrp1/Sh3pxd2b/Fzd4/Rcn1/Atf4/Spred3/Fat1/Hif1a/Cyp1b1/Klf4/Sp1/Ptprm/Gdf11/Gli3/Hdac1/Zhx2	26
GO:0033688	GO:0033688	regulation of osteoblast proliferation	6/595	28/22853	0.0000702	0.0046706	0.0038830	Rhoa/Eif2ak2/Ahr/Npr3/Grem1/Ccn1	6
GO:0007015	GO:0007015	actin filament organization	27/595	456/22853	0.0000717	0.0047008	0.0039082	Arhgef10/Tgfbr1/Rnd3/Rhoa/Icam1/Cyfip2/Arf1/Rflnb/Marcks/Lima1/Synpo/Iqgap2/Actg1/Fchsd2/Gas2l3/Nrp1/Pak3/Sh3pxd2b/Dpysl3/Fat1/Pakap/Tgfb3/Lats1/Slit2/Arfip1/Rhobtb3/Actr2	27
GO:1902903	GO:1902903	regulation of supramolecular fiber organization	24/595	389/22853	0.0000956	0.0059165	0.0049189	Arhgef10/Tgfbr1/Rhoa/Mid1/Icam1/Cyfip2/Arf1/Lima1/Synpo/Iqgap2/Actg1/Hdac2/Fchsd2/Nrp1/Pak3/Vbp1/Map1a/Sh3pxd2b/Mid1ip1/Tgfb3/Lats1/Slit2/Arfip1/Actr2	24
GO:0031346	GO:0031346	positive regulation of cell projection organization	26/595	440/22853	0.0001003	0.0061263	0.0050933	Tgfbr1/Adamts1/Ndel1/Hspa5/Ndrg4/Lif/Ntn1/Marcks/Gpc2/Golga2/Map2k2/Creb3l2/Robo2/Nrp1/Pak3/Septin7/Fzd4/Eef1a1/Dpysl3/Golga4/Tgfb3/Il1rap/Rhoq/Setx/Actr2/Tox	26
GO:0006486	GO:0006486	protein glycosylation	15/595	190/22853	0.0001435	0.0077101	0.0064101	Oga/Rxylt1/Gmppb/Tmem59/Ostc/Magt1/Alg14/Pofut2/Pgm3/Pomt2/Tmem258/Stt3a/Rpn1/Galnt11/Gxylt1	15
GO:0010631	GO:0010631	epithelial cell migration	20/595	304/22853	0.0001538	0.0080650	0.0067051	Tgfbr1/Jcad/Rhoa/Adamts9/Rras/Amot/Ephb4/Nrp1/Plk2/Hif1a/Cyp1b1/Klf4/Sp1/Fstl1/Ptprm/Plekhg5/Akt3/Grem1/Slit2/Nr4a1	20
GO:0001649	GO:0001649	osteoblast differentiation	16/595	220/22853	0.0002251	0.0104783	0.0087115	Fbn2/Tob1/Trp53inp2/Rspo2/Ahr/Cebpd/Sh3pxd2b/Tmem64/Atf4/H3f3a/Chrd/Ddx5/Gli3/Grem1/Ccn1/Gabbr1	16
GO:0031669	GO:0031669	cellular response to nutrient levels	15/595	200/22853	0.0002516	0.0113297	0.0094193	Srebf2/Hspa5/Pmaip1/Ireb2/Brsk1/Eif2ak2/Eif2ak3/Sesn2/Cpeb4/Lars/Mapk1/Pdia3/Atf4/Fads1/Tbl2	15
GO:0032956	GO:0032956	regulation of actin cytoskeleton organization	22/595	369/22853	0.0002973	0.0128659	0.0106965	Arhgef10/Tgfbr1/Rnd3/Rhoa/Icam1/Cyfip2/Arf1/Lima1/Synpo/Iqgap2/Actg1/Hdac2/Fchsd2/Nrp1/Pak3/Sh3pxd2b/Tgfb3/Lats1/Slit2/Arfip1/Rhobtb3/Actr2	22
GO:0009743	GO:0009743	response to carbohydrate	15/595	204/22853	0.0003113	0.0133453	0.0110951	Ppp3cb/Icam1/Ccdc186/Pfkl/Osbp/Hmgcr/Kif5b/Cdk16/Sesn2/Hmgn3/Vamp2/Ppp3ca/Zfp36l1/Hif1a/Pfkfb2	15
GO:0048762	GO:0048762	mesenchymal cell differentiation	16/595	236/22853	0.0004919	0.0169392	0.0140830	Tgfbr1/Spry1/Pofut2/Wnt16/Rflnb/Hdac2/Spry2/Nrp1/Mapk1/Usf3/Spred3/Hif1a/Hes1/Ddx5/Tgfb3/Grem1	16
GO:0032535	GO:0032535	regulation of cellular component size	23/595	417/22853	0.0006494	0.0209799	0.0174424	Tmem123/Ndel1/Rhoa/Rab5a/Icam1/Cyfip2/Arf1/Ntn1/Lima1/Arhgap5/Iqgap2/Ahr/Lars/Fchsd2/Nrp1/Pak3/Golga4/Lats1/Npm1/Akt3/Slit2/Arfip1/Actr2	23
GO:0044262	GO:0044262	cellular carbohydrate metabolic process	18/595	291/22853	0.0006703	0.0213444	0.0177454	Stbd1/Idh1/Inpp5a/Ddb1/Pmaip1/Got1/Bpnt2/Stat3/Midn/Sesn2/Abcg2/Gbe1/Nfe2l1/Gyg/Hif1a/Ier3/Supt20/Pfkfb2	18
GO:0009914	GO:0009914	hormone transport	21/595	374/22853	0.0008766	0.0255430	0.0212361	Oga/Ppp3cb/Rab1a/Slc7a5/Lif/Ccdc186/Tm7sf3/Pfkl/Osbp/Hmgcr/Kif5b/Cdk16/Midn/Hmgn3/Vamp2/Ppp3ca/Fzd4/Rab11fip1/Hif1a/Pfkfb2/Gabbr1	21
GO:1903829	GO:1903829	positive regulation of cellular protein localization	17/595	277/22853	0.0010192	0.0285749	0.0237567	Tcaf1/Pmaip1/Tcp1/Lif/Bbc3/Kif5b/Eif2ak3/Fis1/Sesn2/Tcaf2/Gnl3l/Mapk1/Ipo5/Map1a/Stom/Gli3/Npm1	17
GO:0090276	GO:0090276	regulation of peptide hormone secretion	15/595	231/22853	0.0011294	0.0306998	0.0255233	Oga/Ppp3cb/Lif/Tm7sf3/Pfkl/Osbp/Hmgcr/Kif5b/Cdk16/Midn/Hmgn3/Ppp3ca/Hif1a/Pfkfb2/Gabbr1	15
GO:0045454	GO:0045454	cell redox homeostasis	5/595	31/22853	0.0011409	0.0308239	0.0256266	Selenos/Slc2a10/Nnt/Ddit3/Nfe2l1	5
GO:0019318	GO:0019318	hexose metabolic process	16/595	256/22853	0.0011724	0.0311341	0.0258845	Ddb1/Pmaip1/Pofut2/Pfkl/Dcxr/Man1c1/Midn/Sesn2/Cbr2/Fbn1/Atf4/Nfe2l1/Hif1a/Supt20/Pdha1/Pfkfb2	16
GO:1901214	GO:1901214	regulation of neuron death	21/595	383/22853	0.0011803	0.0311341	0.0258845	Inpp5a/Rhoa/Pmaip1/Bbc3/Stat3/Fis1/Elk1/Tmem259/Cpeb4/Aars/Nrp1/Pak3/Ddit3/Atf4/Vps35/Grid2/Hif1a/Tgfb3/Btg2/Nfatc4/Npm1	21
GO:1903532	GO:1903532	positive regulation of secretion by cell	20/595	360/22853	0.0013083	0.0329620	0.0274041	Oga/Ppp3cb/Sec24a/Vip/Rab27b/Tmed10/Rab5a/Lif/Arf1/Tm7sf3/Osbp/Kif5b/Golph3/Cacna1g/Vps35/Hif1a/Tgfb3/Ppia/Pfkfb2/Gabbr1	20
GO:1902850	GO:1902850	microtubule cytoskeleton organization involved in mitosis	11/595	146/22853	0.0015678	0.0376291	0.0312843	Kpnb1/Arhgef10/Spry1/Map4/Ndel1/Rhoa/Cltc/Golga2/Spry2/Plk2/2610002M06Rik	11
GO:0072521	GO:0072521	purine-containing compound metabolic process	21/595	392/22853	0.0015700	0.0376291	0.0312843	Oga/Cs/Rhoa/Acat1/Pfkl/Hmgcr/Stat3/Dpyd/Crot/Slc27a3/Pnp/Gnai3/Htr2a/Adcy1/Prpsap2/Hif1a/Ier3/Pdha1/Pfkfb2/Rhoq/Prps1	21
GO:1990928	GO:1990928	response to amino acid starvation	6/595	49/22853	0.0016413	0.0387128	0.0321852	Eif2ak2/Eif2ak3/Sesn2/Lars/Mapk1/Atf4	6
GO:0043555	GO:0043555	regulation of translation in response to stress	4/595	21/22853	0.0019133	0.0415627	0.0345546	Dnajc3/Eif2ak3/Sesn2/Npm1	4
GO:0032233	GO:0032233	positive regulation of actin filament bundle assembly	7/595	68/22853	0.0019217	0.0415627	0.0345546	Arhgef10/Tgfbr1/Rhoa/Synpo/Nrp1/Sh3pxd2b/Tgfb3	7
GO:0090162	GO:0090162	establishment of epithelial cell polarity	5/595	35/22853	0.0020011	0.0428894	0.0356576	Rhoa/Myo9a/Golph3/Fat1/Hes1	5
GO:0034599	GO:0034599	cellular response to oxidative stress	16/595	271/22853	0.0021004	0.0448021	0.0372478	Adnp2/Selenos/Pycr1/Ptprk/Wnt16/Prkra/Sesn2/Hdac2/Mapk1/Atf4/Nfe2l1/Hif1a/Sod3/Cyp1b1/Ppia/Setx	16
GO:0019693	GO:0019693	ribose phosphate metabolic process	20/595	376/22853	0.0021804	0.0459502	0.0382023	Cs/Rhoa/Acat1/Pfkl/Hmgcr/Stat3/Dpyd/Crot/Slc27a3/Pnp/Gnai3/Htr2a/Adcy1/Prpsap2/Hif1a/Ier3/Pdha1/Pfkfb2/Rhoq/Prps1	20
GO:0051054	GO:0051054	positive regulation of DNA metabolic process	14/595	223/22853	0.0022294	0.0462108	0.0384190	Oga/Parm1/Tcp1/Kmt5b/Mapk1/Pak3/Pnp/Cyp1b1/Klf4/Npm1/Grem1/Actr2/Eya4/Tox	14
GO:0043271	GO:0043271	negative regulation of ion transport	12/595	176/22853	0.0022867	0.0462108	0.0384190	Vip/Grk6/Icam1/Tcaf2/Ahr/Htr1b/Atf4/Htr2a/Hes1/Kcne4/Calm3/Gabbr1	12
GO:0061299	GO:0061299	retina vasculature morphogenesis in camera-type eye	3/595	11/22853	0.0024786	0.0474233	0.0394270	Nrp1/Fzd4/Cyp1b1	3

24h auxin on AID-Ogt cells - CC down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0030135	GO:0030135	coated vesicle	30/595	199/22838	0.0000000	0.0000000	0.0000000	Copb2/Kdelr2/Sec24d/Sec24a/Copg1/Sec31a/Rab27b/Tmed10/Copa/Lman1/Sar1a/Arf1/Copz2/Sec23a/Yipf5/Copz1/Cltc/Golga2/Copb1/Clint1/Kdelr3/Tmed9/Vamp2/Ece1/Vti1b/Golga5/Sec23ip/Gga2/Dipk2a/Uso1	30
GO:0030120	GO:0030120	vesicle coat	14/595	54/22838	0.0000000	0.0000000	0.0000000	Copb2/Sec24d/Sec24a/Copg1/Sec31a/Copa/Sar1a/Copz2/Sec23a/Copz1/Cltc/Copb1/Clint1/Dipk2a	14
GO:0000139	GO:0000139	Golgi membrane	26/595	267/22838	0.0000000	0.0000005	0.0000004	Copb2/Kdelr2/Scfd1/Copg1/Rab1a/Tmed10/Lman1/Arf1/Sec23a/Osbp/Golim4/Rab6a/Man1c1/Qsox2/Golga2/Kdelr3/Creb3l2/Slc35b1/Glg1/Ndfip1/Gnai3/Golga5/Arfgef2/Dipk2a/Arfip1/Uso1	26
GO:0062023	GO:0062023	collagen-containing extracellular matrix	25/595	393/22838	0.0000424	0.0009509	0.0007858	Lgalsl/Col12a1/Adamts1/Fbn2/Fam20b/Lman1/Adamts5/Aspn/Ntn1/Gpc6/Gpc2/Col5a2/Col23a1/Col1a2/Col11a2/Fbn1/Plxdc2/Atrnl1/Sod3/Gpc4/Tgfb3/Ogn/Ccn1/Slit2/Adamts10	25
GO:0098978	GO:0098978	glutamatergic synapse	20/595	319/22838	0.0002923	0.0062655	0.0051772	Ppp3cb/Flrt3/Rhoa/Clstn1/Atp2b1/Apba1/Synpo/Nrp1/Pak3/Plat/Ppp2r1a/Plppr4/Ppp3ca/Fzd4/Vps35/Grid2/Adcy1/Gpc4/Tamalin/Il1rap	20
GO:0016607	GO:0016607	nuclear speck	19/595	343/22838	0.0017795	0.0240451	0.0198686	Rbm14/Rbm39/Luc7l2/Srrm2/Prx/Son/Nrde2/Prcc/Ccnl1/Ckap4/Lhpp/Fbxl4/Hif1a/Fto/Brd2/Dazap2/Nfatc4/Gli3/Npm1	19
GO:0030027	GO:0030027	lamellipodium	12/595	174/22838	0.0020904	0.0264246	0.0218348	Rhoa/Myo9b/Amot/Palld/Fgd4/Iqgap2/Dpysl3/Fat1/Arhgef6/Ptprm/Plekhg5/Actr2	12
GO:0001527	GO:0001527	microfibril	3/595	13/22838	0.0041403	0.0443737	0.0366662	Fbn2/Fbn1/Adamts10	3

24h auxin on AID-Ogt cells - MF down
ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count

48h auxin on AID-Ogt cells - BP down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:1904951	GO:1904951	positive regulation of establishment of protein localization	27/481	333/22853	0.0000000	0.0000037	0.0000032	Oga/Ppp3cb/Ipo5/Ppia/Tcp1/Tgfb3/Ptgs2/Flna/Tcaf2/Tcaf1/Tomm70a/Pmaip1/Actr3/Cct8/Tmed10/Golph3/Mapk1/Cct3/Cct5/Malrd1/Arf1/Dnm1l/Cct6a/Unc13b/Ppm1a/Sar1a/Sh3glb1	27
GO:1904816	GO:1904816	positive regulation of protein localization to chromosome, telomeric region	7/481	13/22853	0.0000000	0.0000037	0.0000032	Tcp1/Gnl3/Cct8/Gnl3l/Cct3/Cct5/Cct6a	7
GO:0048660	GO:0048660	regulation of smooth muscle cell proliferation	17/481	178/22853	0.0000002	0.0001343	0.0001139	Cnn1/Rhoa/Htr1b/Tgfb3/Vip/Ptgs2/Shc1/Hmgcr/Tpm1/Pdgfd/Sf1/Adamts1/Tert/Gnai3/Ern1/Pik3ca/Ctnnbip1	17
GO:0072594	GO:0072594	establishment of protein localization to organelle	27/481	415/22853	0.0000003	0.0001343	0.0001139	Kpnb1/Ipo5/Ufm1/Tcp1/Vps37a/Tomm40/Hspa4/Tspan17/Ptgs2/Flna/Nxt2/Tomm70a/Pmaip1/Cct8/Nup93/Mapk1/Tert/Ssr3/Cct3/Srp54a/Sec61b/E2f3/Cct5/Srp9/Cct6a/Ddx5/Sh3glb1	27
GO:0007015	GO:0007015	actin filament organization	28/481	456/22853	0.0000005	0.0001891	0.0001604	Rhoa/Acta1/Arpc5/Actg1/Lima1/Tmsb4x/Dpysl3/Dstn/Arhgef10/Ccn2/Tgfb3/Tgfbr1/Coro6/Flna/Tpm1/Tnfaip1/Cfl2/Actr3/Rnd3/Msrb1/Pdxp/Srf/Myo5a/Arf1/Rflnb/Swap70/Actr2/Pik3ca	28
GO:0032535	GO:0032535	regulation of cellular component size	26/481	417/22853	0.0000010	0.0002793	0.0002369	Tmem123/Rhoa/Arpc5/Akt3/Lima1/Tmsb4x/Dstn/Picalm/Rab5a/Npm1/Tnfrsf12a/Tpm1/Cfl2/Actr3/Pdxp/Srf/Prkg2/Lars/Arf1/Wdr36/Swap70/Chmp3/Ndel1/Actr2/Fgf13/Pik3ca	26
GO:0006888	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	13/481	116/22853	0.0000010	0.0002793	0.0002369	Copb2/Vcp/Lman1/Rab1a/Kdelr2/Sec22a/Tmed10/Copg1/Scfd1/Arf1/Yif1b/Sar1a/Spast	13
GO:0006891	GO:0006891	intra-Golgi vesicle-mediated transport	7/481	27/22853	0.0000011	0.0002793	0.0002369	Copb2/Copz1/Rab6a/Copz2/Copg1/Cog5/Vti1b	7
GO:0051222	GO:0051222	positive regulation of protein transport	22/481	317/22853	0.0000012	0.0002826	0.0002397	Oga/Ppp3cb/Ipo5/Ppia/Tgfb3/Ptgs2/Flna/Tcaf2/Tcaf1/Tomm70a/Pmaip1/Actr3/Tmed10/Golph3/Mapk1/Malrd1/Arf1/Dnm1l/Unc13b/Ppm1a/Sar1a/Sh3glb1	22
GO:1901998	GO:1901998	toxin transport	8/481	43/22853	0.0000028	0.0005588	0.0004739	Copb2/Tcp1/Copz1/Cct8/Cct3/Cct5/Scfd1/Cct6a	8
GO:0055001	GO:0055001	muscle cell development	17/481	219/22853	0.0000043	0.0006909	0.0005860	Ldb3/Afg3l2/Acta1/Actg1/Map2k4/Hdac2/Pbrm1/Slc25a4/Pdlim5/Tpm1/Cav2/Tomm70a/Cfl2/Dmd/Srf/Itgb1/Rgs2	17
GO:1902903	GO:1902903	regulation of supramolecular fiber organization	23/481	389/22853	0.0000098	0.0011531	0.0009779	Rhoa/Arpc5/Actg1/Lima1/Tmsb4x/Dstn/Vbp1/Arhgef10/Ccn2/Tgfb3/Tgfbr1/Flna/Hdac2/Tpm1/Cfl2/Actr3/Pdxp/Mid1ip1/Arf1/Swap70/Actr2/Fgf13/Pik3ca	23
GO:0006486	GO:0006486	protein glycosylation	15/481	190/22853	0.0000129	0.0013350	0.0011322	Oga/Rxylt1/Gxylt1/Alg14/Magt1/Ostc/Pmm2/Rpn2/Large1/Ext1/Gmppb/C1galt1c1/Tmem258/Ddost/Alg10b	15
GO:2001233	GO:2001233	regulation of apoptotic signaling pathway	23/481	403/22853	0.0000172	0.0016146	0.0013694	Inhba/Slc25a5/Ppia/Pea15a/Tgfbr1/Ptgs2/Hdac2/Tnfrsf12a/Pdia3/Hdac1/Pmaip1/Selenos/Prkra/Ivns1abp/Ppp2r1a/Tert/Gnai3/Skil/Bcl10/Dnm1l/Vdac2/Pik3cb/Sh3glb1	23
GO:0009100	GO:0009100	glycoprotein metabolic process	20/481	331/22853	0.0000271	0.0024361	0.0020661	Oga/Rxylt1/Gxylt1/Alg14/Bpnt2/Magt1/Rab1a/Fam20b/Ostc/Pmm2/Rpn2/Large1/Ext1/Golph3/Adamts12/Gmppb/C1galt1c1/Tmem258/Ddost/Alg10b	20
GO:0032956	GO:0032956	regulation of actin cytoskeleton organization	21/481	369/22853	0.0000413	0.0031413	0.0026642	Rhoa/Arpc5/Actg1/Lima1/Tmsb4x/Dstn/Arhgef10/Ccn2/Tgfb3/Tgfbr1/Flna/Hdac2/Tpm1/Cfl2/Actr3/Rnd3/Pdxp/Arf1/Swap70/Actr2/Pik3ca	21
GO:0022411	GO:0022411	cellular component disassembly	22/481	402/22853	0.0000489	0.0034920	0.0029616	Oga/Abce1/Eif5a2/Ufm1/Vcp/Slc25a5/Lima1/Dstn/Tgfb3/Tgfbr1/Slc25a4/Tpm1/Cfl2/Pdxp/Mid1ip1/Wipi1/Dnm1l/Swap70/Ndel1/Fgf13/Pik3ca/Spast	22
GO:1902850	GO:1902850	microtubule cytoskeleton organization involved in mitosis	12/481	146/22853	0.0000635	0.0043082	0.0036538	Kpnb1/Rhoa/Vcp/Arhgef10/Map4/Flna/Spry1/Zfp207/Itgb1/Ndel1/Stil/Spast	12
GO:0051656	GO:0051656	establishment of organelle localization	22/481	411/22853	0.0000678	0.0044547	0.0037781	Kpnb1/Abce1/Picalm/Rab1a/Rab27b/Map4/Npm1/Spry1/Ap3m1/Hook3/Actr3/Tmed10/Copg1/Wipi1/Itgb1/Myo5a/Arf1/Ndel1/Actr2/Actr10/Sar1a/Spast	22
GO:0051054	GO:0051054	positive regulation of DNA metabolic process	15/481	223/22853	0.0000827	0.0050980	0.0043237	Oga/Tcp1/Blm/Gnl3/Npm1/Kmt5b/Cct8/Mapk1/Cct3/Cct5/Smchd1/Dhx36/Cct6a/Usp7/Actr2	15
GO:0045933	GO:0045933	positive regulation of muscle contraction	7/481	51/22853	0.0000911	0.0053357	0.0045253	Rhoa/Ccn2/Ptgs2/F2r/Srf/Sphk1/Rgs2	7
GO:0043244	GO:0043244	regulation of protein-containing complex disassembly	11/481	129/22853	0.0000916	0.0053357	0.0045253	Oga/Eif5a2/Lima1/Dstn/Tpm1/Cfl2/Pdxp/Mid1ip1/Swap70/Fgf13/Pik3ca	11
GO:0030239	GO:0030239	myofibril assembly	8/481	69/22853	0.0000986	0.0055913	0.0047420	Ldb3/Acta1/Actg1/Hdac2/Tpm1/Cfl2/Srf/Itgb1	8
GO:0034976	GO:0034976	response to endoplasmic reticulum stress	16/481	255/22853	0.0001098	0.0059000	0.0050038	Ufm1/Vcp/Tmem259/Dnajc3/Derl1/Pdia3/Tbl2/Ccdc47/Pmaip1/Selenos/Rnf103/Sec61b/Canx/Ern1/Gorasp2/Tmem117	16
GO:0006936	GO:0006936	muscle contraction	18/481	312/22853	0.0001216	0.0064503	0.0054706	Rhoa/Cacna2d1/Ccn2/Npy1r/Ptgs2/Shc1/Flna/Tpm1/Dmd/Atp1b1/F2r/Srf/Atp2b1/Sphk1/Fgf13/Pik3ca/Rgs2/Setd3	18
GO:0051653	GO:0051653	spindle localization	7/481	56/22853	0.0001666	0.0083079	0.0070460	Kpnb1/Map4/Spry1/Actr3/Itgb1/Ndel1/Actr2	7
GO:0045765	GO:0045765	regulation of angiogenesis	17/481	302/22853	0.0002487	0.0107401	0.0091088	Akt3/Rras/Pgk1/Jcad/Vash2/Cd59a/Sh2b3/Shc1/Tnfrsf12a/Amot/Lif/Adamts1/Tert/Itgb1/Bmper/Sphk1/Pik3cb	17
GO:0048872	GO:0048872	homeostasis of number of cells	19/481	360/22853	0.0002502	0.0107401	0.0091088	Ppp3cb/Hspa9/Inhba/Slc25a5/Akt3/Exoc6/Sh2b3/Rcor1/Pmaip1/Ext1/F2r/Srf/Ireb2/Skil/Rps24/Bcl10/Myct1/Cfh/Pik3cb	19
GO:0098656	GO:0098656	anion transmembrane transport	13/481	194/22853	0.0002518	0.0107401	0.0091088	Grk6/Slc25a5/Slc25a29/Slc7a5/Slc35b1/Tcaf2/Slc25a4/Slc25a13/Tcaf1/Slc26a2/Itgb1/Vdac2/Rgs2	13
GO:0048588	GO:0048588	developmental cell growth	16/481	275/22853	0.0002598	0.0107522	0.0091190	Map2k4/Picalm/Tnfrsf12a/Slc25a4/Pdlim5/Tomm70a/Actr3/Ext1/Srf/Itgb1/Wdr36/Ndel1/Fgf13/Flrt3/Rgs2/Sh3glb1	16
GO:0090288	GO:0090288	negative regulation of cellular response to growth factor stimulus	9/481	104/22853	0.0003528	0.0133949	0.0113603	Cd59a/Spry1/Adamts12/Sost/Skil/Bmper/Ppm1a/Fstl3/Pik3cb	9
GO:0022613	GO:0022613	ribonucleoprotein complex biogenesis	20/481	411/22853	0.0004942	0.0177831	0.0150820	Rpl7/Abce1/Ddx54/Nhp2/Rps16/Dis3/Npm1/Rpsa/Ncl/Nop56/Luc7l2/Rpl14/Gnl3l/Eif5/Mrto4/Rps24/Wdr36/Rplp0/Rpl10/Tsr2	20
GO:1903522	GO:1903522	regulation of blood circulation	15/481	264/22853	0.0005138	0.0181712	0.0154112	Rhoa/Cacna2d1/Ccn2/Npy1r/Ptgs2/Shc1/Flna/Hmgcr/Tpm1/Dmd/Atp1b1/F2r/Atp2b1/Fgf13/Rgs2	15
GO:1903792	GO:1903792	negative regulation of anion transport	5/481	33/22853	0.0005901	0.0205203	0.0174034	Grk6/Htr1b/Tcaf2/Prkg2/Rgs2	5
GO:0060537	GO:0060537	muscle tissue development	22/481	482/22853	0.0006250	0.0211988	0.0179789	Rhoa/Acta1/Map2k4/Maff/Tgfbr1/Meg3/Hdac2/Slc25a4/Pdlim5/Schip1/Hmgcr/Tpm1/Cav2/Tomm70a/Cfl2/Dmd/Mapk1/Srf/Skil/Itgb1/Ddx5/Rgs2	22
GO:0050821	GO:0050821	protein stabilization	12/481	190/22853	0.0007303	0.0227721	0.0193132	Tcp1/Rassf1/Npm1/Flna/Prkra/Cct8/Zfp207/Atp1b1/Cct3/Cct5/Cct6a/Usp7	12
GO:0007339	GO:0007339	binding of sperm to zona pellucida	6/481	52/22853	0.0007557	0.0230261	0.0195286	Tcp1/Cct8/Cct3/Cct5/Cct6a/Vdac2	6
GO:0016236	GO:0016236	macroautophagy	13/481	222/22853	0.0009027	0.0249013	0.0211190	Stbd1/Ufm1/Vcp/Slc25a5/Rab1a/Slc25a4/Gnai3/Wipi1/Scfd1/Myo5a/Vti1b/Trp53inp2/Sh3glb1	13
GO:0010720	GO:0010720	positive regulation of cell development	18/481	377/22853	0.0011516	0.0299693	0.0254172	Picalm/Flna/Hdac2/Tnfrsf12a/Map2k2/Cyp51/Hdac1/Lif/Actr3/Lims1/Srf/Skil/Dhx36/Dnm1l/Rheb/Ndel1/Actr2/Sh3glb1	18
GO:0001558	GO:0001558	regulation of cell growth	20/481	450/22853	0.0014928	0.0361250	0.0306380	Adnp2/Rhoa/Inhba/Picalm/Tgfbr1/Npm1/Tnfrsf12a/Slc25a4/Tomm70a/Adipor1/Actr3/Srf/Rbbp7/Sphk1/Wdr36/Ndel1/Igfbp7/Fgf13/Rgs2/Sh3glb1	20
GO:0003018	GO:0003018	vascular process in circulatory system	13/481	235/22853	0.0015110	0.0361421	0.0306524	Rhoa/Htr1b/Npy1r/Ptgs2/Shc1/Amot/Hmgcr/Ext1/Abcg2/F2r/Atp2b1/Rgs2/Ctnnbip1	13
GO:0036465	GO:0036465	synaptic vesicle recycling	7/481	81/22853	0.0015932	0.0376724	0.0319503	Ppp3cb/Actg1/Picalm/Rab5a/Rab27b/Dnm1l/Canx	7
GO:0060324	GO:0060324	face development	6/481	61/22853	0.0017586	0.0402788	0.0341608	Rras/Tgfb3/Map2k2/Schip1/Mapk1/Srf	6
GO:0050805	GO:0050805	negative regulation of synaptic transmission	7/481	83/22853	0.0018354	0.0408212	0.0346208	Htr1b/Rap1b/Ptgs2/Grid2/Srf/Myo5a/Arf1	7
GO:0035592	GO:0035592	establishment of protein localization to extracellular region	18/481	395/22853	0.0019267	0.0417417	0.0354015	Oga/Ppp3cb/Ppia/Tgfb3/Hmgn3/Cdk16/Cyp51/Hmgcr/Tmed10/Golph3/Copg1/F2r/Malrd1/Myo5a/Arf1/Dnm1l/Unc13b/Tmem167	18
GO:0060998	GO:0060998	regulation of dendritic spine development	7/481	84/22853	0.0019667	0.0419197	0.0355524	Hdac2/Sdk1/Actr3/Dhx36/Arf1/Dnm1l/Actr2	7
GO:0035051	GO:0035051	cardiocyte differentiation	11/481	186/22853	0.0020261	0.0419197	0.0355524	Map2k4/Hdac2/Pbrm1/Slc25a4/Pdlim5/Tomm70a/Mapk1/Srf/Itgb1/Dhx36/Rgs2	11
GO:0030168	GO:0030168	platelet activation	7/481	86/22853	0.0022511	0.0442621	0.0375391	Ppia/Sh2b3/F2r/Srf/C1galt1c1/Cfh/Pik3cb	7
GO:0001942	GO:0001942	hair follicle development	8/481	111/22853	0.0024225	0.0459838	0.0389993	Inhba/Gorab/Ptgs2/Hdac2/Hdac1/Ext1/Nsun2/Myo5a	8
GO:0003301	GO:0003301	physiological cardiac muscle hypertrophy	5/481	45/22853	0.0024707	0.0462623	0.0392354	Map2k4/Slc25a4/Pdlim5/Tomm70a/Rgs2	5
GO:0061049	GO:0061049	cell growth involved in cardiac muscle cell development	5/481	45/22853	0.0024707	0.0462623	0.0392354	Map2k4/Slc25a4/Pdlim5/Tomm70a/Rgs2	5

48h auxin on AID-Ogt cells - CC down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0140534	GO:0140534	endoplasmic reticulum protein-containing complex	14/483	128/22838	0.0000006	0.0001443	0.0001106	Hsd17b12/Vcp/Alg14/Srebf2/Magt1/Derl1/Ostc/Pdia3/Rpn2/Selenos/Sec61b/Tmem258/Ern1/Ddost	14
GO:0005832	GO:0005832	chaperonin-containing T-complex	5/483	10/22838	0.0000010	0.0001607	0.0001232	Tcp1/Cct8/Cct3/Cct5/Cct6a	5
GO:0005798	GO:0005798	Golgi-associated vesicle	11/483	88/22838	0.0000025	0.0002516	0.0001929	Copb2/Zdhhc13/Copz1/Rab27b/Copz2/Kdelr2/Tmed10/Copg1/Scfd1/Arf1/Erc2	11
GO:0000139	GO:0000139	Golgi membrane	19/483	267/22838	0.0000046	0.0002921	0.0002239	Copb2/Zdhhc13/Lman1/Rab1a/Golim4/Slc35b1/Qsox2/Rab6a/Kdelr2/Actr3/Tmed10/Copg1/Gnai3/Scfd1/Rab2a/Arf1/Dnm1l/Gorasp2/Yif1b	19
GO:0005838	GO:0005838	proteasome regulatory particle	6/483	23/22838	0.0000064	0.0003296	0.0002527	Psmd14/Psmd1/Psmd3/Psmd7/Psmd13/Psmd2	6
GO:1905369	GO:1905369	endopeptidase complex	9/483	70/22838	0.0000163	0.0006204	0.0004756	Vcp/Psmd14/Psmd1/Psma2/Psma1/Psmd3/Psmd7/Psmd13/Psmd2	9
GO:0022626	GO:0022626	cytosolic ribosome	11/483	110/22838	0.0000219	0.0006204	0.0004756	Rpl7/Rps23/Rps16/Rpsa/Rpl14/Rpl15/Rps10/Rps24/Rpl8/Rplp0/Rpl10	11
GO:0030016	GO:0030016	myofibril	16/483	222/22838	0.0000222	0.0006204	0.0004756	Rpl7/Ppp3cb/Myl9/Ldb3/Acta1/Actg1/Lman1/Palld/Flna/Pdlim5/Tpm1/Cfl2/Rpl15/Dmd/Fhl3/Arf1	16
GO:0030126	GO:0030126	COPI vesicle coat	4/483	12/22838	0.0000855	0.0017948	0.0013757	Copb2/Copz1/Copz2/Copg1	4
GO:0001725	GO:0001725	stress fiber	9/483	88/22838	0.0001023	0.0018408	0.0014109	Myl9/Ldb3/Acta1/Lima1/Palld/Pdlim5/Amot/Tpm1/Fhl3	9
GO:0001726	GO:0001726	ruffle	11/483	153/22838	0.0004261	0.0056512	0.0043316	Rhoa/Lima1/Jcad/Rab5a/Tnfrsf12a/Amot/Tpm1/Actr3/Pdxp/Itgb1/Myo5a	11
GO:0098984	GO:0098984	neuron to neuron synapse	17/483	359/22838	0.0017924	0.0194192	0.0148848	Rpl7/Cnn3/Picalm/Map4/Pdlim5/Rpl14/Dmd/Grid2/Rpl8/Rnf19a/Rheb/Unc13b/Rplp0/Plcb4/Actr2/Flrt3/Erc2	17
GO:0045121	GO:0045121	membrane raft	18/483	393/22838	0.0019207	0.0197862	0.0151661	Slc25a5/Pgk1/Tgfbr1/Rab5a/Ptgs2/Slc25a4/Cav2/Abcg2/Dmd/Gja3/Mapk1/Atp1b1/F2r/Atp2b1/Gnai3/Itgb1/Bcl10/Vdac2	18
GO:0046930	GO:0046930	pore complex	4/483	26/22838	0.0020417	0.0201765	0.0154653	Slc25a5/Tomm40/Slc25a4/Vdac2	4
GO:0098562	GO:0098562	cytoplasmic side of membrane	11/483	194/22838	0.0029150	0.0277197	0.0212472	Litaf/Rhoa/Esyt1/Rab5a/Cdk16/Map2k2/Cav2/Atp2b1/Gnai3/Gnb2/Rgs2	11
GO:0016581	GO:0016581	NuRD complex	3/483	16/22838	0.0042881	0.0357630	0.0274123	Hdac2/Hdac1/Rbbp7	3
GO:0090545	GO:0090545	CHD-type complex	3/483	16/22838	0.0042881	0.0357630	0.0274123	Hdac2/Hdac1/Rbbp7	3
GO:0014069	GO:0014069	postsynaptic density	15/483	328/22838	0.0044872	0.0364456	0.0279355	Rpl7/Cnn3/Picalm/Map4/Pdlim5/Rpl14/Dmd/Grid2/Rpl8/Rheb/Rplp0/Plcb4/Actr2/Flrt3/Erc2	15
GO:0030055	GO:0030055	cell-substrate junction	10/483	180/22838	0.0051213	0.0403300	0.0309129	Lima1/Palld/Map2k2/Cav2/Actr3/Dmd/Lims1/Mapk1/Itgb1/Flrt3	10
GO:0031965	GO:0031965	nuclear membrane	12/483	242/22838	0.0056462	0.0430929	0.0330307	Kpnb1/Tmem97/Ptgs2/Txnl4a/Osbpl3/Cav2/Nup93/Nucb2/Prkg2/Ern1/Cenpv/Spast	12

48h auxin on AID-Ogt cells - MF down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0003779	GO:0003779	actin binding	24/473	444/22360	0.0000295	0.0034254	0.0029501	Cnn1/Ldb3/Arpc5/Lima1/Tmsb4x/Dstn/Palld/Cnn3/Vash2/Fxyd5/Coro6/Tagln/Flna/Pdlim5/Tpm1/Cfl2/Actr3/Msrb1/Dmd/Itgb1/Fhl3/Myo5a/Actr2/Setd3	24
GO:0019003	GO:0019003	GDP binding	9/473	79/22360	0.0000436	0.0037757	0.0032518	Rhoa/Rras/Rap1b/Rab5a/Rab27b/Gnai3/Rab2a/Arf1/Rheb	9
GO:0016671	GO:0016671	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	4/473	11/22360	0.0000580	0.0041046	0.0035350	Pdia3/Msrb1/Msra/Msrb3	4
GO:0015215	GO:0015215	nucleotide transmembrane transporter activity	4/473	23/22360	0.0012722	0.0430772	0.0371000	Slc25a5/Slc25a17/Slc25a4/Abcc4	4

4d auxin on AID-Ogt cells - BP down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0006888	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	24/663	116/22853	0.0000000	0.0000000	0.0000000	Copb2/Lman1/Rab1a/Vcp/Sec24d/Tmed10/Scfd1/Golga2/Sec23a/Kdelr2/Sec24a/Copg1/Yipf5/Sec31a/Bet1/Tmed9/Tmed2/Yif1b/Creb3l2/Tmed7/Arf1/Copb1/Sec16a/Sec22a	24
GO:1904951	GO:1904951	positive regulation of establishment of protein localization	36/663	333/22853	0.0000000	0.0000000	0.0000000	Oga/Ipo5/Tgfb3/Ppp3cb/Tcp1/Ppia/Actr3/Flna/Cct6a/Tmed10/Dnm1l/Ptgs2/Cct5/Tomm70a/Kif5b/Vps35/Tcaf2/Arf6/Sec24a/Rack1/Mapk1/Hras/Pmaip1/Tardbp/Malrd1/Hsp90ab1/Cct8/Pak1/Pfkfb2/Glrx/Cct3/Arf1/Oxct1/Emd/Frmd4a/Pdcd10	36
GO:0022613	GO:0022613	ribonucleoprotein complex biogenesis	40/663	411/22853	0.0000000	0.0000000	0.0000000	Rpl7/Abce1/Npm1/Rpl6/Rpl3/Rps16/Eif2s2/Rpsa/Dis3/Rps24/Rpl14/Rbmx/Ltv1/Ddx54/Rplp0/Ncl/Rpl7a/Nmd3/Ptbp2/Eif4b/Nhp2/Gnl3l/Luc7l2/Wdr43/Lsm4/Rcl1/Hsp90ab1/Rps19/Mrto4/Dcaf13/Ddx3x/Nop56/Tsr1/Efl1/Eif3a/Setx/Tsr2/Rps5/Rpl24/Ebna1bp2	40
GO:1903829	GO:1903829	positive regulation of cellular protein localization	31/663	277/22853	0.0000000	0.0000001	0.0000001	Ipo5/Tcp1/Npm1/Actr3/Flna/Cct6a/Ptgs2/Cct5/Kif5b/Nmd3/Tcaf2/Tfrc/Arf6/Gnl3l/Rack1/Mapk1/Hras/Rock2/Pmaip1/Gnl3/Tardbp/Hnrnpk/Hsp90ab1/Cav2/Cct8/Pak1/Cct3/Map1a/Larp7/Nptn/Lif	31
GO:0007015	GO:0007015	actin filament organization	41/663	456/22853	0.0000000	0.0000001	0.0000001	Actg1/Arpc5/Tgfb3/Tmsb4x/Cfl2/Tpm1/Rhoa/Dpysl3/Arhgef10/Actr3/Tgfbr1/Flna/Actr2/Msrb1/Tnfaip1/Tpm2/Srf/Lima1/Rnd3/Coro6/Nrp1/Wdr1/Dstn/Swap70/Arf6/Rflnb/Myadm/Pakap/Flii/Arpc4/Rock2/Tpm4/Sh3pxd2b/Pls3/Ccn2/Pak1/Cobl/Rhobtb3/Pdxp/Iqgap2/Arf1	41
GO:0034248	GO:0034248	regulation of cellular amide metabolic process	40/663	446/22853	0.0000000	0.0000002	0.0000001	Abce1/Otud6b/Npm1/Eif5a2/Picalm/Paip2b/Tmed10/Rps9/Dnajc3/Stat3/Ncl/Eif3e/Gapdh/Igf2bp3/Syncrip/Rack1/Mapk1/Polr2g/Rock2/Tardbp/Cnbp/Rps3a1/Rplp1/Aars/Cpeb4/Tmed2/Rpl22/Calr/Eprs/Ddx3x/Elavl1/Rgs2/Srp9/Etf1/Cnot6/Pdk1/Cnot11/Eif4e/Dhx36/Sphk1	40
GO:0032956	GO:0032956	regulation of actin cytoskeleton organization	34/663	369/22853	0.0000000	0.0000012	0.0000010	Actg1/Arpc5/Tgfb3/Tmsb4x/Cfl2/Tpm1/Rhoa/Arhgef10/Actr3/Tgfbr1/Flna/Actr2/Hdac2/Lima1/Rnd3/Nrp1/Wdr1/Dstn/Swap70/Ntrk3/Arf6/Myadm/Flii/Ilk/Arpc4/Hras/Rock2/Sh3pxd2b/Ccn2/Pak1/Rhobtb3/Pdxp/Iqgap2/Arf1	34
GO:0051222	GO:0051222	positive regulation of protein transport	31/663	317/22853	0.0000000	0.0000013	0.0000011	Oga/Ipo5/Tgfb3/Ppp3cb/Ppia/Actr3/Flna/Tmed10/Dnm1l/Ptgs2/Tomm70a/Kif5b/Vps35/Tcaf2/Arf6/Sec24a/Rack1/Mapk1/Hras/Pmaip1/Tardbp/Malrd1/Hsp90ab1/Pak1/Pfkfb2/Glrx/Arf1/Oxct1/Emd/Frmd4a/Pdcd10	31
GO:0031346	GO:0031346	positive regulation of cell projection organization	37/663	440/22853	0.0000000	0.0000024	0.0000019	Tgfb3/Dpysl3/Picalm/Actr3/Tgfbr1/Flna/Actr2/Rpl4/Srf/Dnm1l/Golga2/Ndel1/Eef1a1/Adamts1/Septin7/Nrp1/Ntrk3/Ilk/Hras/Map2k1/Hnrnpk/Rap1a/Pak1/Hspa5/Creb3l2/Rgs2/Cobl/Nptn/Lif/Map2k2/Rhoq/Il1rap/Dhx36/Dmd/Setx/Sphk1/Tnfrsf12a	37
GO:0032535	GO:0032535	regulation of cellular component size	35/663	417/22853	0.0000000	0.0000053	0.0000043	Tmem123/Arpc5/Tmsb4x/Cfl2/Tpm1/Npm1/Rhoa/Picalm/Actr3/Rab5a/Actr2/Rpl4/Lars/Srf/Lima1/Ndel1/Nrp1/Wdr1/Dstn/Swap70/Ntrk3/Arf6/Myadm/Arhgap5/Flii/Ilk/Arpc4/Hsp90ab1/Pak1/Fgf13/Pdxp/Iqgap2/Arf1/Chmp3/Tnfrsf12a	35
GO:1901998	GO:1901998	toxin transport	11/663	43/22853	0.0000000	0.0000061	0.0000049	Copb2/Tcp1/Copz1/Cct6a/Scfd1/Cct5/Nrp1/Cct8/Hspa5/Antxr2/Cct3	11
GO:0022411	GO:0022411	cellular component disassembly	33/663	402/22853	0.0000001	0.0000179	0.0000144	Oga/Abce1/Ufm1/Tgfb3/Slc25a5/Cfl2/Tpm1/Slc25a4/Vcp/Eif5a2/Tgfbr1/Pbxip1/Lima1/Dnm1l/Mid1ip1/Golga2/Ndel1/Kif5b/Septin7/Mid1/Wdr1/Dstn/Swap70/Arf6/Vps4b/Flii/Snai2/Sh3pxd2b/Fgf13/Etf1/Map1a/Pdxp/Setx	33
GO:0055001	GO:0055001	muscle cell development	22/663	219/22853	0.0000005	0.0000730	0.0000586	Ldb3/Actg1/Cfl2/Map2k4/Tpm1/Slc25a4/Afg3l2/Hdac2/Pdlim5/Pbrm1/Srf/Tomm70a/Adm/Wdr1/Flii/Ctdp1/Cav2/Pak1/Ccn4/Rgs2/Dmd/Hes1	22
GO:2001233	GO:2001233	regulation of apoptotic signaling pathway	31/663	403/22853	0.0000009	0.0001229	0.0000986	Slc25a5/Ppia/Selenos/Hdac1/Tgfbr1/Ppp2r1a/Hdac2/Gnai3/Dnm1l/Ptgs2/Vdac2/Qars/Pea15a/Nrp1/Inhba/Rack1/Pmaip1/Map2k1/Itprip/Snai2/Ivns1abp/Hnrnpk/Mnt/Ddx3x/Usp47/Eno1/Cth/Higd1a/Pdia3/Bcl10/Tnfrsf12a	31
GO:0043244	GO:0043244	regulation of protein-containing complex disassembly	16/663	129/22853	0.0000011	0.0001323	0.0001062	Oga/Cfl2/Tpm1/Eif5a2/Lima1/Mid1ip1/Mid1/Wdr1/Dstn/Swap70/Flii/Fgf13/Etf1/Map1a/Pdxp/Setx	16
GO:0048660	GO:0048660	regulation of smooth muscle cell proliferation	19/663	178/22853	0.0000011	0.0001347	0.0001081	Cnn1/Htr1b/Tgfb3/Tpm1/Rhoa/Shc1/Pdgfd/Gnai3/Vip/Ptgs2/Adamts1/Hmgcr/Ilk/Sf1/Zfp143/Nppb/Pak1/Ccn4/Ereg	19
GO:0048588	GO:0048588	developmental cell growth	24/663	275/22853	0.0000018	0.0001921	0.0001542	Map2k4/Slc25a4/Vcl/Picalm/Actr3/Rpl4/Pdlim5/Srf/Ndel1/Tomm70a/Septin7/Nrp1/Ntrk3/Ilk/Ctdp1/Flrt3/Hnrnpk/Hsp90ab1/Pak1/Fgf13/Ccn4/Rgs2/Cobl/Tnfrsf12a	24
GO:0010720	GO:0010720	positive regulation of cell development	29/663	377/22853	0.0000021	0.0002137	0.0001715	Cyp51/Hdac1/Picalm/Actr3/Flna/Actr2/Rpl4/Lims1/Hdac2/Srf/Dnm1l/Golga2/Ndel1/Nrp1/Ntrk3/Myadm/Ilk/Map2k1/Tgm2/Pak1/Calr/Akap11/Nptn/Lif/Map2k2/Dhx36/Nap1l1/Hes1/Tnfrsf12a	29
GO:0030307	GO:0030307	positive regulation of cell growth	20/663	206/22853	0.0000026	0.0002593	0.0002081	Adnp2/Slc25a4/Rhoa/Picalm/Tgfbr1/Rpl4/Srf/Ndel1/Nrp1/Ntrk3/Ilk/Hnrnpk/Pak1/Ddx3x/Ccn4/Usp47/Derl2/H3f3a/Sphk1/Tnfrsf12a	20
GO:0072594	GO:0072594	establishment of protein localization to organelle	30/663	415/22853	0.0000049	0.0004220	0.0003387	Kpnb1/Ufm1/Ipo5/Tcp1/Nxt2/Hspa4/Flna/Cct6a/Tomm40/Ptgs2/Stat3/Cct5/Srp54c/Tomm70a/Vps37a/Rab10/Ddx5/Ssr3/Mapk1/Pmaip1/Tardbp/Hsp90ab1/Cct8/Hspa5/Calm3/Elavl1/Srp9/Cct3/Hk1/Nedd4	30
GO:0006936	GO:0006936	muscle contraction	25/663	312/22853	0.0000052	0.0004220	0.0003387	Cacna2d1/Tpm1/Rhoa/Flna/Shc1/Tpm2/Srf/Ptgs2/Aldoa/Acta2/Myl6/Rock2/Tpm4/Map2k1/Ccn2/Npy1r/Calm3/Fgf13/Rgs2/Eno1/F2r/Htr2a/Dmd/Sphk1/Atp2b1	25
GO:0071692	GO:0071692	protein localization to extracellular region	29/663	402/22853	0.0000074	0.0005098	0.0004091	Oga/Tgfb3/Ppp3cb/Ppia/Cyp51/Tmed10/Dnm1l/Pfkl/Fbn1/Fbn2/Klf7/Hmgn3/Kif5b/Vps35/Hmgcr/Rab10/Arf6/Sec24a/Copg1/Tardbp/Tmem167/Malrd1/Pfkfb2/Glrx/Arf1/Midn/F2r/Oxct1/Frmd4a	29
GO:0045933	GO:0045933	positive regulation of muscle contraction	9/663	51/22853	0.0000141	0.0008365	0.0006714	Rhoa/Srf/Ptgs2/Map2k1/Ccn2/Rgs2/Eno1/F2r/Sphk1	9
GO:0009100	GO:0009100	glycoprotein metabolic process	25/663	331/22853	0.0000144	0.0008410	0.0006750	Oga/Rab1a/Ostc/Chst12/Rxylt1/Gmppb/Pmm2/Ddost/Stt3a/Bpnt2/Magt1/Tmem258/Alg14/Itm2a/Adamts12/Pgm3/Fam20b/Gxylt1/Ganab/Eogt/Alg10b/Mgat2/Rpn2/Dsel/Hs6st2	25
GO:0032386	GO:0032386	regulation of intracellular transport	25/663	334/22853	0.0000167	0.0009208	0.0007391	Ufm1/Ipo5/Nsun2/Actr3/Flna/Scfd1/Ptgs2/Ndel1/Kif5b/Tcaf2/Snx12/Mapk1/Hras/Pmaip1/Tardbp/Map2k1/Yipf5/Hsp90ab1/Pak1/Derl2/Arf1/Map2k2/Emd/Nedd4/Pdcd10	25
GO:0034976	GO:0034976	response to endoplasmic reticulum stress	21/663	255/22853	0.0000193	0.0010102	0.0008108	Ufm1/Vcp/Selenos/Dnajc3/Rnft1/Usp14/Canx/Manf/Tmem259/Pmaip1/Tmed2/Calr/Hspa5/Ddx3x/Gorasp2/Creb3l2/Derl2/Derl1/Pdia3/Sec16a/Bak1	21
GO:0042176	GO:0042176	regulation of protein catabolic process	27/663	390/22853	0.0000312	0.0014830	0.0011903	Cyp51/Vcp/Psmd1/Flna/Rnft1/Vip/Psmd14/Pdcl3/Vps35/Usp14/Hmgcr/Snx12/Ecscr/Psmd2/Rack1/Usp5/Tmem259/Arih1/Ddb1/Azin1/Hsp90ab1/Trib2/Dda1/Map1a/Psmd3/Wwp1/Nedd4	27
GO:0003301	GO:0003301	physiological cardiac muscle hypertrophy	8/663	45/22853	0.0000402	0.0016663	0.0013374	Map2k4/Slc25a4/Pdlim5/Tomm70a/Ctdp1/Pak1/Ccn4/Rgs2	8
GO:0061049	GO:0061049	cell growth involved in cardiac muscle cell development	8/663	45/22853	0.0000402	0.0016663	0.0013374	Map2k4/Slc25a4/Pdlim5/Tomm70a/Ctdp1/Pak1/Ccn4/Rgs2	8
GO:0035150	GO:0035150	regulation of tube size	16/663	172/22853	0.0000435	0.0017418	0.0013980	Htr1b/Rhoa/Shc1/Ptgs2/Adm/Hmgcr/Acta2/Manf/Sod3/Rock2/Map2k1/Npy1r/Rgs2/F2r/Htr2a/Atp2b1	16
GO:0019693	GO:0019693	ribose phosphate metabolic process	26/663	376/22853	0.0000444	0.0017613	0.0014136	Cs/Atp5pb/Pgk1/Rhoa/Vcp/Gnai3/Stat3/Pfkl/Acat1/Ctps/Prps1/Gapdh/Hmgcr/Slc25a13/Aldoa/Pdha1/Map2k1/Nppb/Pfkfb2/Eno1/Pdk1/Efl1/Htr2a/Hk1/Rhoq/Prxl2c	26
GO:0006520	GO:0006520	cellular amino acid metabolic process	20/663	255/22853	0.0000601	0.0021602	0.0017338	Psat1/Gcsh/Tarsl2/Lars/Oat/Acat1/Ctps/Qars/Got1/Aars/Apip/Azin1/Eprs/Nars/Plod2/Yars/Cth/Pycr1/Bcat2/Hsd17b10	20
GO:0003018	GO:0003018	vascular process in circulatory system	19/663	235/22853	0.0000608	0.0021669	0.0017392	Htr1b/Rhoa/Shc1/Ptgs2/Abcg2/Adm/Hmgcr/Acta2/Manf/Sod3/Rock2/Map2k1/Nppb/Npy1r/Rgs2/F2r/Htr2a/Slc2a1/Atp2b1	19
GO:0072521	GO:0072521	purine-containing compound metabolic process	26/663	392/22853	0.0000882	0.0029049	0.0023316	Oga/Cs/Atp5pb/Pgk1/Rhoa/Vcp/Gnai3/Stat3/Pfkl/Acat1/Prps1/Gapdh/Hmgcr/Slc25a13/Aldoa/Pdha1/Map2k1/Nppb/Pfkfb2/Eno1/Pdk1/Efl1/Htr2a/Hk1/Rhoq/Prxl2c	26
GO:0071560	GO:0071560	cellular response to transforming growth factor beta stimulus	18/663	227/22853	0.0001205	0.0036433	0.0029242	Tgfb3/Actr3/Tgfbr1/Spred3/Pdgfd/Stat3/Fbn1/Aspn/Fbn2/Spry1/Got1/Hsp90ab1/Cav2/Hspa5/Tgfb1i1/Col1a2/Scx/Ptprk	18
GO:0060485	GO:0060485	mesenchyme development	21/663	292/22853	0.0001365	0.0039423	0.0031642	Tgfb3/Tgfbr1/Flna/Spred3/Hdac2/Spry1/Nrp1/Ddx5/Rflnb/Phactr4/Mapk1/Hnrnpab/Rock2/Meox1/Snai2/Tgfb1i1/Scx/Usf3/Nedd4/Hes1/Fam172a	21
GO:0006486	GO:0006486	protein glycosylation	16/663	190/22853	0.0001420	0.0039885	0.0032012	Oga/Ostc/Rxylt1/Gmppb/Pmm2/Ddost/Stt3a/Magt1/Tmem258/Alg14/Pgm3/Gxylt1/Eogt/Alg10b/Mgat2/Rpn2	16
GO:0050821	GO:0050821	protein stabilization	16/663	190/22853	0.0001420	0.0039885	0.0032012	Tcp1/Npm1/Flna/Cct6a/Atf7ip/Cct5/Pdcl3/Naa15/Gapdh/Hsp90ab1/Cct8/Calr/Zfp207/Cct3/Sec16a/Pdcd10	16
GO:0045773	GO:0045773	positive regulation of axon extension	8/663	54/22853	0.0001541	0.0042885	0.0034421	Rpl4/Srf/Ndel1/Nrp1/Ntrk3/Ilk/Pak1/Tnfrsf12a	8
GO:0006753	GO:0006753	nucleoside phosphate metabolic process	28/663	455/22853	0.0001711	0.0046492	0.0037315	Oga/Cs/Atp5pb/Pgk1/Rhoa/Vcp/Gnai3/Stat3/Pfkl/Acat1/Ctps/Prps1/Gapdh/Hmgcr/Slc25a13/Aldoa/Mapk1/Pdha1/Map2k1/Nppb/Pfkfb2/Eno1/Pdk1/Efl1/Htr2a/Hk1/Rhoq/Prxl2c	28
GO:0045927	GO:0045927	positive regulation of growth	22/663	320/22853	0.0001820	0.0049159	0.0039456	Adnp2/Slc25a4/Rhoa/Picalm/Tgfbr1/Rpl4/Srf/Ndel1/Nrp1/Ntrk3/Mapk1/Ilk/Sh3pxd2b/Hnrnpk/Pak1/Ddx3x/Ccn4/Usp47/Derl2/H3f3a/Sphk1/Tnfrsf12a	22
GO:0006096	GO:0006096	glycolytic process	10/663	91/22853	0.0003065	0.0073241	0.0058785	Pgk1/Stat3/Pfkl/Gapdh/Aldoa/Pfkfb2/Eno1/Htr2a/Hk1/Prxl2c	10
GO:0060996	GO:0060996	dendritic spine development	12/663	128/22853	0.0003565	0.0081062	0.0065062	Actr3/Actr2/Hdac2/Pdlim5/Dnm1l/Septin7/Arf6/Hnrnpk/Pak1/Sdk1/Arf1/Dhx36	12
GO:0060324	GO:0060324	face development	8/663	61/22853	0.0003651	0.0082086	0.0065884	Tgfb3/Rras/Srf/Schip1/Mapk1/Map2k1/Scx/Map2k2	8
GO:0010639	GO:0010639	negative regulation of organelle organization	23/663	363/22853	0.0004231	0.0091951	0.0073802	Slc25a5/Tmsb4x/Tpm1/Rps6ka2/Npm1/Scfd1/Lima1/Dnm1l/Mid1ip1/Map4/Mid1/Swap70/Tfrc/Myadm/Gnl3l/Flii/Fgf13/Zfp207/Map1a/Higd1a/Tom1l1/Lif/H3f3a	23
GO:0032331	GO:0032331	negative regulation of chondrocyte differentiation	5/663	24/22853	0.0005441	0.0110869	0.0088986	Tgfbr1/Rflnb/Adamts12/Snai2/Ccn4	5
GO:0060560	GO:0060560	developmental growth involved in morphogenesis	19/663	280/22853	0.0005743	0.0115608	0.0092789	Vcl/Picalm/Actr3/Rpl4/Srf/Ndel1/Spry1/Septin7/Nrp1/Ntrk3/Ilk/Flrt3/Hnrnpk/Hsp90ab1/Pak1/Tnc/Fgf13/Cobl/Tnfrsf12a	19
GO:0009896	GO:0009896	positive regulation of catabolic process	28/663	494/22853	0.0006373	0.0126472	0.0101509	Slc25a5/Slc25a4/Vcp/Gnai3/Rnft1/Vip/Trp53inp2/Vps35/Ecscr/Rack1/Usp5/Tmem259/Polr2g/Nnt/Rock2/Arih1/Tardbp/Map2k1/Ddb1/Trib2/Dda1/Trim12c/Cnot6/Wwp1/Htr2a/Dhx36/Nedd4/Prxl2c	28
GO:0007339	GO:0007339	binding of sperm to zona pellucida	7/663	52/22853	0.0007213	0.0138858	0.0111451	Tcp1/Cct6a/Vdac2/Cct5/Aldoa/Cct8/Cct3	7
GO:0051645	GO:0051645	Golgi localization	4/663	15/22853	0.0007424	0.0138858	0.0111451	Golga2/Copg1/Hook3/Pdcd10	4
GO:1903522	GO:1903522	regulation of blood circulation	18/663	264/22853	0.0007505	0.0139325	0.0111825	Cacna2d1/Tpm1/Rhoa/Flna/Shc1/Ptgs2/Adm/Hmgcr/Map2k1/Ccn2/Npy1r/Calm3/Fgf13/Rgs2/F2r/Htr2a/Dmd/Atp2b1	18
GO:0010811	GO:0010811	positive regulation of cell-substrate adhesion	12/663	139/22853	0.0007510	0.0139325	0.0111825	Rras/Hsd17b12/Flna/Hacd1/Lims1/Nrp1/Itga5/Myadm/Ilk/Rsu1/Calr/Dmd	12
GO:0030968	GO:0030968	endoplasmic reticulum unfolded protein response	8/663	68/22853	0.0007676	0.0140125	0.0112467	Selenos/Dnajc3/Tmed2/Hspa5/Creb3l2/Derl2/Derl1/Bak1	8
GO:0060425	GO:0060425	lung morphogenesis	8/663	68/22853	0.0007676	0.0140125	0.0112467	Srf/Spry1/Mapk1/Map2k1/Tnc/Kras/Lif/Map2k2	8
GO:0016052	GO:0016052	carbohydrate catabolic process	12/663	140/22853	0.0008002	0.0143111	0.0114864	Stbd1/Pgk1/Stat3/Pfkl/Gapdh/Aldoa/Ldha/Pfkfb2/Eno1/Htr2a/Hk1/Prxl2c	12
GO:0045981	GO:0045981	positive regulation of nucleotide metabolic process	6/663	39/22853	0.0008409	0.0144704	0.0116142	Vcp/Stat3/Map2k1/Eno1/Htr2a/Prxl2c	6
GO:0030239	GO:0030239	myofibril assembly	8/663	69/22853	0.0008465	0.0144704	0.0116142	Ldb3/Actg1/Cfl2/Tpm1/Hdac2/Srf/Wdr1/Flii	8
GO:0051881	GO:0051881	regulation of mitochondrial membrane potential	9/663	86/22853	0.0008679	0.0145632	0.0116887	Oga/Vcp/Clic1/Rack1/Got1/Nnt/Pmaip1/Pycr1/Bak1	9
GO:0099173	GO:0099173	postsynapse organization	15/663	203/22853	0.0009008	0.0147920	0.0118724	Actr3/Actr2/Pdlim5/Dnm1l/Vps35/Septin7/Nrp1/Ntrk3/Arf6/Rock2/Hnrnpk/Grid2/Arf1/Il1rap/Dhx36	15
GO:1903532	GO:1903532	positive regulation of secretion by cell	22/663	360/22853	0.0009010	0.0147920	0.0118724	Oga/Tgfb3/Ppp3cb/Ppia/Rab5a/Tmed10/Vip/Dnm1l/Kif5b/Vps35/Arf6/Sec24a/Vps4b/Tardbp/Malrd1/Pfkfb2/Glrx/Arf1/Lif/Oxct1/Frmd4a/Sphk1	22
GO:0060537	GO:0060537	muscle tissue development	27/663	482/22853	0.0009413	0.0152340	0.0122271	Cfl2/Map2k4/Tpm1/Slc25a4/Rhoa/Tgfbr1/Hdac2/Pdlim5/Srf/Schip1/Tomm70a/Hmgcr/Myl6/Ddx5/Mapk1/Ctdp1/Adamts9/Maff/Cav2/Pak1/Ccn4/Rgs2/Scx/Meg3/Emd/Dmd/Foxn2	27
GO:1903580	GO:1903580	positive regulation of ATP metabolic process	6/663	40/22853	0.0009653	0.0152748	0.0122598	Vcp/Stat3/Map2k1/Eno1/Htr2a/Prxl2c	6
GO:0000054	GO:0000054	ribosomal subunit export from nucleus	4/663	16/22853	0.0009672	0.0152748	0.0122598	Abce1/Npm1/Ltv1/Nmd3	4
GO:0033750	GO:0033750	ribosome localization	4/663	16/22853	0.0009672	0.0152748	0.0122598	Abce1/Npm1/Ltv1/Nmd3	4
GO:0071869	GO:0071869	response to catecholamine	8/663	71/22853	0.0010240	0.0157895	0.0126730	Htr1b/Flna/Gnai3/Vps35/Mapk1/Tgm2/Cav2/Htr2a	8
GO:0048678	GO:0048678	response to axon injury	8/663	72/22853	0.0011233	0.0168090	0.0134912	Dpysl3/Flna/Ndel1/Ntrk3/Map2k1/Flrt3/Tnc/Map2k2	8
GO:1901215	GO:1901215	negative regulation of neuron death	17/663	254/22853	0.0012728	0.0182869	0.0146775	Tgfb3/Map2k4/Npm1/Rhoa/Inpp5a/Stat3/Vps35/Nrp1/Rack1/Tmem259/Ilk/Hras/Aars/Hsp90ab1/Cpeb4/F2r/Kras	17
GO:0035987	GO:0035987	endodermal cell differentiation	5/663	29/22853	0.0013489	0.0190008	0.0152504	Col5a2/Col12a1/Itga5/Inhba/Leo1	5
GO:0045765	GO:0045765	regulation of angiogenesis	19/663	302/22853	0.0014071	0.0194011	0.0155718	Pgk1/Rras/Shc1/Stat3/Pdcl3/Jcad/Adamts1/Sh2b3/Adm/Nrp1/Cd59a/Itga5/Ecscr/F3/Rock2/Adamts9/Lif/Sphk1/Tnfrsf12a	19
GO:1903034	GO:1903034	regulation of response to wounding	13/663	170/22853	0.0014221	0.0194085	0.0155776	Actg1/Flna/Ndel1/Sh2b3/Hmgcr/Acta2/Ntrk3/Hras/Map2k1/Ccn4/F2r/Map2k2/Tnfrsf12a	13
GO:0071478	GO:0071478	cellular response to radiation	13/663	172/22853	0.0015800	0.0209629	0.0168253	Npm1/Eef1d/Tnks1bp1/Rnf4/Elk1/Hras/Ddb1/Snai2/Usp47/Bak1/Dhx36/Nedd4/Ptprk	13
GO:0050807	GO:0050807	regulation of synapse organization	17/663	263/22853	0.0018469	0.0238112	0.0191114	Rhoa/Vcp/Picalm/Actr3/Actr2/Pdlim5/Dnm1l/Vps35/Ntrk3/Arf6/Flrt3/Hnrnpk/Grid2/Lrrn3/Il1rap/Dhx36/Nedd4	17
GO:0032965	GO:0032965	regulation of collagen biosynthetic process	6/663	46/22853	0.0020341	0.0259313	0.0208130	Tgfb3/Got1/Ccn2/Rap1a/Scx/F2r	6
GO:0022604	GO:0022604	regulation of cell morphogenesis	20/663	337/22853	0.0021320	0.0268799	0.0215744	Tpm1/Rhoa/Picalm/Actr3/Flna/Actr2/Lims1/Dnm1l/Rnd3/Aldoa/Nrp1/Wdr1/Myadm/Pakap/Ilk/Hnrnpk/Calr/Rhobtb3/Rhoq/Dhx36	20
GO:0014812	GO:0014812	muscle cell migration	10/663	117/22853	0.0021773	0.0272247	0.0218511	Arpc5/Tmsb4x/Tpm1/Rhoa/Pdgfd/Adamts1/F3/Ilk/Pak1/Ccn4	10
GO:0090270	GO:0090270	regulation of fibroblast growth factor production	3/663	10/22853	0.0025043	0.0300056	0.0240831	Ptgs2/Cd59a/Rock2	3
GO:0050805	GO:0050805	negative regulation of synaptic transmission	8/663	83/22853	0.0028056	0.0323460	0.0259615	Htr1b/Srf/Ptgs2/Rap1a/Rap1b/Grid2/Arf1/Htr2a	8
GO:0043555	GO:0043555	regulation of translation in response to stress	4/663	21/22853	0.0028349	0.0323460	0.0259615	Npm1/Dnajc3/Tmed2/Ddx3x	4
GO:0090162	GO:0090162	establishment of epithelial cell polarity	5/663	35/22853	0.0031961	0.0356258	0.0285940	Rhoa/Arf6/Cyth3/Frmd4a/Hes1	5
GO:0010001	GO:0010001	glial cell differentiation	16/663	254/22853	0.0032004	0.0356258	0.0285940	Rhoa/Hdac1/Arhgef10/Actr3/Hdac2/Stat3/Wdr1/Ntrk3/Mapk1/Ilk/Map2k1/Prx/Kras/Lif/Dmd/Hes1	16
GO:1903427	GO:1903427	negative regulation of reactive oxygen species biosynthetic process	4/663	22/22853	0.0033863	0.0365424	0.0293297	Rhoa/Stat3/Eef1a1/Abcb7	4
GO:0062013	GO:0062013	positive regulation of small molecule metabolic process	12/663	166/22853	0.0033957	0.0365424	0.0293297	Srebf2/Vcp/Mid1ip1/Ptgs2/Stat3/Lpgat1/Pmaip1/Map2k1/Ddb1/Eno1/Htr2a/Prxl2c	12
GO:1902850	GO:1902850	microtubule cytoskeleton organization involved in mitosis	11/663	146/22853	0.0036059	0.0380077	0.0305057	Kpnb1/Rhoa/Vcp/Arhgef10/Flna/Golga2/Ndel1/Spry1/Map4/Vps4b/Zfp207	11
GO:0010563	GO:0010563	negative regulation of phosphorus metabolic process	24/663	454/22853	0.0037063	0.0387079	0.0310677	Ppia/Npm1/Hspa4/Dnajc3/Stat3/Spry1/Sh2b3/Qars/Hmgcr/Swap70/Ntrk3/Myadm/Ctdsp2/Rack1/Ilk/Nnt/Rock2/Tardbp/Tmed2/Rgs2/Midn/Stk39/Bak1/Dmd	24
GO:0030728	GO:0030728	ovulation	4/663	23/22853	0.0040063	0.0407228	0.0326850	Ptgs2/Adamts1/Inhba/Ereg	4
GO:1903800	GO:1903800	positive regulation of production of miRNAs involved in gene silencing by miRNA	3/663	12/22853	0.0043967	0.0425136	0.0341223	Ddx5/Map2k1/Map2k2	3
GO:0019439	GO:0019439	aromatic compound catabolic process	23/663	435/22853	0.0044290	0.0427361	0.0343008	Npm1/Vcp/Nsun2/Dis3/Acat1/Xrn2/Eif3e/Syncrip/Snd1/Ddx5/Polr2g/Rock2/Tardbp/Lsm4/Aldh1l2/Mrto4/Elavl1/Etf1/Pon2/Cnot6/Pdxp/Cnot11/Dhx36	23
GO:0034446	GO:0034446	substrate adhesion-dependent cell spreading	9/663	109/22853	0.0044817	0.0429636	0.0344834	Rhoa/Rab1a/Flna/Lims1/Nrp1/Myadm/Ilk/Calr/Atrnl1	9
GO:0098656	GO:0098656	anion transmembrane transport	13/663	194/22853	0.0044903	0.0429636	0.0344834	Slc7a5/Slc26a2/Grk6/Slc25a5/Slc25a4/Vdac2/Tcaf2/Slc35b1/Slc25a13/Rgs2/Slc7a1/Hk1/Slc3a2	13
GO:0044270	GO:0044270	cellular nitrogen compound catabolic process	22/663	412/22853	0.0047370	0.0446908	0.0358697	Npm1/Vcp/Nsun2/Dis3/Acat1/Xrn2/Eif3e/Syncrip/Snd1/Ddx5/Polr2g/Rock2/Tardbp/Lsm4/Aldh1l2/Mrto4/Elavl1/Etf1/Cnot6/Pdxp/Cnot11/Dhx36	22
GO:0002183	GO:0002183	cytoplasmic translational initiation	4/663	25/22853	0.0054672	0.0492154	0.0395012	Eif2s2/Eif4a1/Eif4b/Eif3a	4
GO:1902683	GO:1902683	regulation of receptor localization to synapse	4/663	25/22853	0.0054672	0.0492154	0.0395012	Hras/Map2k1/Rap1a/Nptn	4
GO:0048538	GO:0048538	thymus development	6/663	56/22853	0.0055274	0.0493678	0.0396236	Tgfbr1/Srf/Mapk1/Map2k1/Map2k2/Hes1	6
GO:0051653	GO:0051653	spindle localization	6/663	56/22853	0.0055274	0.0493678	0.0396236	Kpnb1/Actr3/Actr2/Ndel1/Spry1/Map4	6
GO:0010611	GO:0010611	regulation of cardiac muscle hypertrophy	7/663	74/22853	0.0056182	0.0495011	0.0397306	Slc25a4/Tomm70a/Rock2/Ctdp1/Pak1/Ccn4/Rgs2	7

4d auxin on AID-Ogt cells - CC down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0022626	GO:0022626	cytosolic ribosome	27/669	110/22838	0.0000000	0.0000000	0.0000000	Rpl7/Rps23/Rpl6/Rpl3/Rps16/Rpl4/Rps9/Rpl8/Rpl15/Rpsa/Rps24/Rpl14/Rps4x/Rplp0/Rps10/Rpl7a/Rps3a1/Rplp1/Rpl9/Rps19/Rpl22/Rpl18/Ddx3x/Rplp2/Rpl13/Rps5/Rpl24	27
GO:0043292	GO:0043292	contractile fiber	28/669	235/22838	0.0000000	0.0000000	0.0000000	Rpl7/Myl9/Ldb3/Actg1/Lman1/Palld/Ppp3cb/Cfl2/Tpm1/Rpl6/Vcl/Flna/Rpl4/Rpl15/Pdlim5/Tpm2/Fhl3/Aldoa/Acta2/Ilk/Trpc1/Pak1/Calm3/Sync/Arf1/Pdlim7/Slc2a1/Dmd	28
GO:0030016	GO:0030016	myofibril	27/669	222/22838	0.0000000	0.0000000	0.0000000	Rpl7/Myl9/Ldb3/Actg1/Lman1/Palld/Ppp3cb/Cfl2/Tpm1/Rpl6/Vcl/Flna/Rpl4/Rpl15/Pdlim5/Tpm2/Fhl3/Aldoa/Ilk/Trpc1/Pak1/Calm3/Sync/Arf1/Pdlim7/Slc2a1/Dmd	27
GO:0030135	GO:0030135	coated vesicle	23/669	199/22838	0.0000000	0.0000010	0.0000008	Copb2/Lman1/Sec24d/Picalm/Copz1/Tmed10/Golga2/Sec23a/Vti1b/Kdelr2/Sec24a/Copg1/Copz2/Yipf5/Sec31a/Tmed9/Tmed2/Yif1b/Tmed7/Clint1/Arf1/Copb1/Sec16a	23
GO:0001725	GO:0001725	stress fiber	15/669	88/22838	0.0000000	0.0000013	0.0000010	Myl9/Ldb3/Palld/Tpm1/Vcl/Pdlim5/Lima1/Fhl3/Septin7/Acta2/Ilk/Lpp/Tpm4/Daam1/Pdlim7	15
GO:0140534	GO:0140534	endoplasmic reticulum protein-containing complex	18/669	128/22838	0.0000000	0.0000013	0.0000010	Srebf2/Vcp/Ostc/Selenos/Hsd17b12/Emc2/Ddost/Stt3a/Magt1/Tmem258/Alg14/Calr/Hspa5/Ganab/Derl2/Rpn2/Derl1/Pdia3	18
GO:0030055	GO:0030055	cell-substrate junction	21/669	180/22838	0.0000001	0.0000025	0.0000020	Palld/Vcl/Actr3/Lims1/Lima1/Nrp1/Itga5/Mapk1/Ilk/Lpp/Rsu1/Map2k1/Cpne3/Flrt3/Cav2/Pak1/Tln1/Tgfb1i1/Pdlim7/Map2k2/Dmd	21
GO:0001726	GO:0001726	ruffle	18/669	153/22838	0.0000006	0.0000127	0.0000098	Tpm1/Rhoa/Actr3/Rab5a/Lima1/Jcad/Eef1a1/Itga5/Arf6/Myadm/Cyth3/Pak1/Cobl/Pdxp/Tln1/Pdlim7/Myo9b/Tnfrsf12a	18
GO:0005938	GO:0005938	cell cortex	26/669	305/22838	0.0000013	0.0000245	0.0000189	Rhoa/Flna/Actr2/Exoc6/Rnd3/Eef1a1/Ncl/Septin7/Wdr1/Dstn/Arf6/Myadm/Tpm4/Map2k1/Ccn2/Hnrnpk/Eno1/Cobl/Rhobtb3/Crip2/Slc2a1/Map2k2/Myo9b/Emd/Nedd4/Dmd	26
GO:0030120	GO:0030120	vesicle coat	10/669	54/22838	0.0000033	0.0000600	0.0000463	Copb2/Sec24d/Copz1/Sec23a/Sec24a/Copg1/Copz2/Sec31a/Clint1/Copb1	10
GO:0005832	GO:0005832	chaperonin-containing T-complex	5/669	10/22838	0.0000047	0.0000817	0.0000630	Tcp1/Cct6a/Cct5/Cct8/Cct3	5
GO:0014069	GO:0014069	postsynaptic density	22/669	328/22838	0.0002939	0.0029789	0.0022987	Rpl7/Cnn3/Rpl6/Picalm/Actr2/Rpl8/Pdlim5/Rpl14/Rplp0/Vps35/Map4/Flrt3/Hnrnpk/Rps19/Cpeb4/Pak1/Grid2/Plppr4/Map1a/Nptn/Eif3a/Dmd	22
GO:0005838	GO:0005838	proteasome regulatory particle	5/669	23/22838	0.0004612	0.0044986	0.0034714	Psmd1/Psmd14/Psmd2/Psmd7/Psmd3	5
GO:0046930	GO:0046930	pore complex	5/669	26/22838	0.0008384	0.0071058	0.0054833	Slc25a5/Slc25a4/Tomm40/Vdac2/Bak1	5
GO:0098984	GO:0098984	neuron to neuron synapse	22/669	359/22838	0.0009842	0.0079752	0.0061541	Rpl7/Cnn3/Rpl6/Picalm/Actr2/Rpl8/Pdlim5/Rpl14/Rplp0/Vps35/Map4/Flrt3/Hnrnpk/Rps19/Cpeb4/Pak1/Grid2/Plppr4/Map1a/Nptn/Eif3a/Dmd	22
GO:1905369	GO:1905369	endopeptidase complex	8/669	70/22838	0.0009916	0.0079752	0.0061541	Vcp/Psmd1/Psma2/Psmd14/Usp14/Psmd2/Psmd7/Psmd3	8
GO:0005852	GO:0005852	eukaryotic translation initiation factor 3 complex	4/669	16/22838	0.0010027	0.0079752	0.0061541	Eif3e/Ddx3x/Eif3j2/Eif3a	4
GO:0045121	GO:0045121	membrane raft	23/669	393/22838	0.0014050	0.0105276	0.0081237	Slc25a5/Pgk1/Slc25a4/Vcl/Tgfbr1/Rab5a/Gnai3/Ptgs2/Vdac2/Abcg2/Myadm/Mapk1/Trpc1/Cav2/F2r/Kras/Slc2a1/Hk1/Rhoq/Nedd4/Dmd/Bcl10/Atp2b1	23
GO:0098562	GO:0098562	cytoplasmic side of membrane	14/669	194/22838	0.0018031	0.0127702	0.0098543	Esyt1/Rhoa/Litaf/Gnb2/Rab5a/Gnai3/Cyth3/Cav2/Rgs2/Rnf31/Kras/Map2k2/Aspscr1/Atp2b1	14
GO:0031616	GO:0031616	spindle pole centrosome	4/669	20/22838	0.0024321	0.0159167	0.0122822	Npm1/Spout1/Rock2/Emd	4
GO:0031968	GO:0031968	organelle outer membrane	14/669	205/22838	0.0029940	0.0184273	0.0142196	Slc25a4/Cyb5b/Tomm40/Dnm1l/Ptgs2/Vdac2/Tomm70a/Ntrk3/Itprip/Hk1/Emd/Bak1/Dmd/Armcx3	14
GO:0031414	GO:0031414	N-terminal protein acetyltransferase complex	3/669	11/22838	0.0034630	0.0198930	0.0153506	Naa15/Naa25/Txnl4a	3
GO:0044295	GO:0044295	axonal growth cone	5/669	42/22838	0.0073828	0.0385545	0.0297509	Flna/Kif5b/Flrt3/Hsp90ab1/Cobl	5

4d auxin on AID-Ogt cells - MF down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0003779	GO:0003779	actin binding	37/655	444/22360	0.0000000	0.0000024	0.0000021	Cnn1/Ldb3/Cnn3/Arpc5/Palld/Tmsb4x/Cfl2/Tpm1/Vcl/Actr3/Flna/Actr2/Msrb1/Pdlim5/Tpm2/Lima1/Fhl3/Tagln/Coro6/Wdr1/Dstn/Phactr4/Flii/Arpc4/Ppp1r18/Tpm4/Pls3/Cobl/Map1a/Tln1/Iqgap2/Daam1/Pdlim7/Myo9b/Sntb2/Emd/Dmd	37
GO:0090079	GO:0090079	translation regulator activity, nucleic acid binding	16/655	101/22360	0.0000000	0.0000041	0.0000035	Eef1g/Eif5a2/Eef1d/Paip2b/Eif2s2/Eif4a1/Eef1a1/Eif3e/Eif4b/Eif1a/Cpeb4/Etf1/Efl1/Eif4e/Eif3a/Eif1ax	16
GO:0019003	GO:0019003	GDP binding	13/655	79/22360	0.0000005	0.0000313	0.0000267	Rras/Rhoa/Rab5a/Gnai3/Srp54c/Rab10/Arf6/Hras/Rap1a/Rap1b/Arf1/Rab18/Kras	13
GO:0051020	GO:0051020	GTPase binding	23/655	313/22360	0.0000554	0.0020526	0.0017524	Kpnb1/Rabggtb/Ipo5/Vcl/Ankfy1/Gnb2/Picalm/Flna/Tnfaip1/Dnm1l/Chml/Gdi2/Rock2/Map2k1/Rap1a/Pak1/Eprs/Eno1/Rhobtb3/Iqgap2/Daam1/Myo9b/Xpot	23
GO:0004812	GO:0004812	aminoacyl-tRNA ligase activity	7/655	41/22360	0.0001693	0.0043271	0.0036943	Tarsl2/Lars/Qars/Aars/Eprs/Nars/Yars	7
GO:0016671	GO:0016671	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	4/655	11/22360	0.0002043	0.0048594	0.0041487	Msrb1/Glrx/Msrb3/Pdia3	4
GO:0008483	GO:0008483	transaminase activity	5/655	24/22360	0.0005685	0.0120352	0.0102751	Psat1/Oat/Got1/Tgm2/Bcat2	5
GO:0043022	GO:0043022	ribosome binding	8/655	69/22360	0.0009006	0.0175612	0.0149929	Eif5a2/Rpsa/Naa15/Rack1/Cpeb4/Hspa5/Rpn2/Efl1	8
GO:0019887	GO:0019887	protein kinase regulator activity	14/655	198/22360	0.0021774	0.0366688	0.0313062	Npm1/Dnajc3/Qars/Rack1/Map2k1/Rplp1/Itprip/Hsp90ab1/Ddx3x/Trib2/Fgf13/Tom1l1/Map2k2/Mob1a	14

4d auxin on ctrl cells - BP down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0016125	GO:0016125	sterol metabolic process	11/108	153/22853	0.0000000	0.0000001	0.0000001	Ldlr/Lss/Dhcr24/Nsdhl/Insig1/Hsd17b7/Hmgcs1/Sqle/Fdps/Fdft1/Lbr	11
GO:1902652	GO:1902652	secondary alcohol metabolic process	11/108	156/22853	0.0000000	0.0000001	0.0000001	Ldlr/Lss/Dhcr24/Nsdhl/Insig1/Hsd17b7/Hmgcs1/Sqle/Fdps/Fdft1/Lbr	11
GO:1901617	GO:1901617	organic hydroxy compound biosynthetic process	11/108	231/22853	0.0000000	0.0000029	0.0000024	Lss/Dhcr24/Nsdhl/Insig1/Hsd17b7/Hmgcs1/Sqle/Stard4/Fdps/Fdft1/Lbr	11
GO:0050658	GO:0050658	RNA transport	8/108	148/22853	0.0000005	0.0000739	0.0000634	Srsf3/Hnrnpa1/Khdrbs1/Eny2/Ybx1/Ran/Tpr/Thoc3	8
GO:0008299	GO:0008299	isoprenoid biosynthetic process	5/108	35/22853	0.0000006	0.0000772	0.0000663	Lss/Idi1/Hmgcs1/Fdps/Fdft1	5
GO:0071426	GO:0071426	ribonucleoprotein complex export from nucleus	5/108	80/22853	0.0000389	0.0032213	0.0027639	Srsf3/Eny2/Ran/Tpr/Thoc3	5
GO:0043062	GO:0043062	extracellular structure organization	8/108	311/22853	0.0001165	0.0067538	0.0057948	Serpinh1/Olfml2b/Fscn1/Col1a1/Fkbp10/Ptx3/Cav1/Col11a1	8
GO:0045229	GO:0045229	external encapsulating structure organization	8/108	312/22853	0.0001191	0.0067538	0.0057948	Serpinh1/Olfml2b/Fscn1/Col1a1/Fkbp10/Ptx3/Cav1/Col11a1	8
GO:0043489	GO:0043489	RNA stabilization	4/108	64/22853	0.0002410	0.0106125	0.0091057	Fus/Hnrnpa0/Ybx1/Hnrnpd	4
GO:0032507	GO:0032507	maintenance of protein location in cell	4/108	69/22853	0.0003220	0.0133151	0.0114245	Insig1/Pfn1/Cav1/Arl2bp	4
GO:0060491	GO:0060491	regulation of cell projection assembly	6/108	202/22853	0.0004010	0.0154704	0.0132738	Cdc42ep3/Fscn1/Pfn1/Anln/Cav1/Gap43	6
GO:0046824	GO:0046824	positive regulation of nucleocytoplasmic transport	4/108	74/22853	0.0004209	0.0154704	0.0132738	Khdrbs1/Xbp1/Ran/Tpr	4
GO:0070542	GO:0070542	response to fatty acid	3/108	33/22853	0.0005051	0.0179034	0.0153614	Ldlr/Scd2/Scd1	3
GO:0032970	GO:0032970	regulation of actin filament-based process	8/108	417/22853	0.0008260	0.0269700	0.0231407	Cdc42ep3/Fscn1/Pfn1/Ctnna2/Cav1/Epha3/Atp2a2/Svil	8
GO:0051169	GO:0051169	nuclear transport	7/108	326/22853	0.0009183	0.0289340	0.0248258	Srsf3/Khdrbs1/Eny2/Xbp1/Ran/Tpr/Thoc3	7
GO:0010873	GO:0010873	positive regulation of cholesterol esterification	2/108	10/22853	0.0009714	0.0296655	0.0254534	Stard4/Scd1	2
GO:0086064	GO:0086064	cell communication by electrical coupling involved in cardiac conduction	2/108	10/22853	0.0009714	0.0296655	0.0254534	Slc8a1/Cav1	2
GO:0009100	GO:0009100	glycoprotein metabolic process	7/108	331/22853	0.0010031	0.0301700	0.0258863	Edem1/Xylt1/Ptx3/B3gnt5/Chsy3/Dpagt1/Col11a1	7
GO:0006984	GO:0006984	ER-nucleus signaling pathway	3/108	43/22853	0.0011040	0.0327066	0.0280627	Ppp1r15b/Insig1/Atp2a2	3
GO:0043434	GO:0043434	response to peptide hormone	7/108	350/22853	0.0013833	0.0381367	0.0327219	Srsf3/Insig1/Srsf5/Ybx1/Cav1/Xbp1/Atp2a2	7
GO:0048705	GO:0048705	skeletal system morphogenesis	6/108	257/22853	0.0014031	0.0381540	0.0327367	Serpinh1/Anxa6/Insig1/Col1a1/Men1/Col11a1	6
GO:1900102	GO:1900102	negative regulation of endoplasmic reticulum unfolded protein response	2/108	13/22853	0.0016683	0.0415759	0.0356727	Xbp1/Pdia6	2

4d auxin on ctrl cells - CC down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0005643	GO:0005643	nuclear pore	4/109	67/22838	0.0002986	0.0486821	0.0423506	Eny2/Lbr/Ran/Tpr	4
GO:0031227	GO:0031227	intrinsic component of endoplasmic reticulum membrane	5/109	157/22838	0.0009472	0.0486821	0.0423506	Scd2/Insig1/Edem1/Scd1/Xbp1	5
GO:0005635	GO:0005635	nuclear envelope	8/109	423/22838	0.0009659	0.0486821	0.0423506	Eny2/Ybx1/Rrm1/Lbr/Epha3/Ran/Tubb5/Tpr	8
GO:0098643	GO:0098643	banded collagen fibril	2/109	11/22838	0.0012070	0.0486821	0.0423506	Col1a1/Col11a1	2

4d auxin on ctrl cells - MF down
	ID	Description	GeneRatio	BgRatio	pvalue	p.adjust	qvalue	geneID	Count
GO:0016717	GO:0016717	oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water	2/104	14/22360	0.0018799	0.0371288	0.0315384	Scd2/Scd1	2
GO:0004659	GO:0004659	prenyltransferase activity	2/104	15/22360	0.0021626	0.0401987	0.0341462	Fdps/Fdft1	2
GO:0032934	GO:0032934	sterol binding	3/104	57/22360	0.0023834	0.0409810	0.0348107	Anxa6/Insig1/Stard4	3
GO:0046982	GO:0046982	protein heterodimerization activity	6/104	307/22360	0.0031430	0.0496600	0.0421829	Tubb2b/Tenm3/Nfyc/Cav1/Xbp1/Ran	6

4.4.3 MSigDb Set Enrichment Test

sessionInfo()

## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] msigdbr_7.5.1               org.Mm.eg.db_3.14.0        
##  [3] AnnotationDbi_1.56.2        clusterProfiler_4.2.2      
##  [5] GeneOverlap_1.30.0          EnhancedVolcano_1.12.0     
##  [7] ggrepel_0.9.2               tidytext_0.3.4             
##  [9] DOSE_3.20.1                 data.table_1.14.6          
## [11] gridExtra_2.3               gplots_3.1.3               
## [13] ggpubr_0.5.0                vsn_3.62.0                 
## [15] reshape2_1.4.4              ggplot2_3.4.0              
## [17] tximport_1.22.0             DESeq2_1.34.0              
## [19] SummarizedExperiment_1.24.0 Biobase_2.54.0             
## [21] MatrixGenerics_1.6.0        matrixStats_0.62.0         
## [23] GenomicRanges_1.46.1        GenomeInfoDb_1.30.1        
## [25] IRanges_2.28.0              S4Vectors_0.32.4           
## [27] BiocGenerics_0.40.0        
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.2             tidyselect_1.2.0       RSQLite_2.2.18        
##   [4] grid_4.1.3             BiocParallel_1.28.3    scatterpie_0.1.8      
##   [7] munsell_0.5.0          codetools_0.2-18       preprocessCore_1.56.0 
##  [10] withr_2.5.0            colorspace_2.0-3       GOSemSim_2.20.0       
##  [13] ggalt_0.4.0            knitr_1.40             rstudioapi_0.14       
##  [16] ggsignif_0.6.4         Rttf2pt1_1.3.11        GenomeInfoDbData_1.2.7
##  [19] polyclip_1.10-4        bit64_4.0.5            farver_2.1.1          
##  [22] downloader_0.4         vctrs_0.5.1            treeio_1.18.1         
##  [25] generics_0.1.3         xfun_0.35              R6_2.5.1              
##  [28] ggbeeswarm_0.6.0       graphlayouts_0.8.3     locfit_1.5-9.6        
##  [31] bitops_1.0-7           cachem_1.0.6           fgsea_1.20.0          
##  [34] gridGraphics_0.5-1     DelayedArray_0.20.0    assertthat_0.2.1      
##  [37] scales_1.2.1           ggraph_2.1.0           enrichplot_1.14.2     
##  [40] beeswarm_0.4.0         gtable_0.3.1           ash_1.0-15            
##  [43] affy_1.72.0            tidygraph_1.2.2        rlang_1.0.6           
##  [46] genefilter_1.76.0      splines_4.1.3          rstatix_0.7.1         
##  [49] extrafontdb_1.0        lazyeval_0.2.2         broom_1.0.1           
##  [52] BiocManager_1.30.22    yaml_2.3.6             abind_1.4-5           
##  [55] backports_1.4.1        qvalue_2.26.0          tokenizers_0.2.3      
##  [58] extrafont_0.18         tools_4.1.3            ggplotify_0.1.0       
##  [61] affyio_1.64.0          jquerylib_0.1.4        RColorBrewer_1.1-3    
##  [64] Rcpp_1.0.9             plyr_1.8.8             zlibbioc_1.40.0       
##  [67] purrr_0.3.5            RCurl_1.98-1.9         viridis_0.6.2         
##  [70] magrittr_2.0.3         DO.db_2.9              SnowballC_0.7.0       
##  [73] patchwork_1.1.2        evaluate_0.18          xtable_1.8-4          
##  [76] XML_3.99-0.12          compiler_4.1.3         tibble_3.1.8          
##  [79] maps_3.4.1             KernSmooth_2.23-20     crayon_1.5.2          
##  [82] shadowtext_0.1.2       htmltools_0.5.3        ggfun_0.0.8           
##  [85] tidyr_1.2.1            geneplotter_1.72.0     aplot_0.1.8           
##  [88] DBI_1.1.3              tweenr_2.0.2           proj4_1.0-11          
##  [91] MASS_7.3-55            babelgene_22.9         Matrix_1.5-3          
##  [94] car_3.1-1              cli_3.4.1              parallel_4.1.3        
##  [97] igraph_1.3.5           pkgconfig_2.0.3        prettydoc_0.4.1       
## [100] ggtree_3.2.1           annotate_1.72.0        vipor_0.4.5           
## [103] bslib_0.4.1            XVector_0.34.0         yulab.utils_0.0.5     
## [106] janeaustenr_1.0.0      stringr_1.4.1          digest_0.6.30         
## [109] Biostrings_2.62.0      rmarkdown_2.18         fastmatch_1.1-3       
## [112] tidytree_0.4.1         gtools_3.9.3           lifecycle_1.0.3       
## [115] nlme_3.1-155           jsonlite_1.8.3         carData_3.0-5         
## [118] viridisLite_0.4.1      limma_3.50.3           fansi_1.0.3           
## [121] pillar_1.8.1           lattice_0.20-45        ggrastr_1.0.1         
## [124] KEGGREST_1.34.0        fastmap_1.1.0          httr_1.4.4            
## [127] survival_3.2-13        GO.db_3.14.0           glue_1.6.2            
## [130] png_0.1-7              bit_4.0.5              ggforce_0.4.1         
## [133] stringi_1.7.8          sass_0.4.2             blob_1.2.3            
## [136] caTools_1.18.2         memoise_2.0.1          dplyr_1.0.10          
## [139] ape_5.6-2

Auxin-treated AID-Ogt MEFs Differential Expression analysis

Sara Formichetti

August 27, 2021