Table 2:

Gene lists enriched in dynamic transcription clusters 2 and 3.

Annotation Term	Identifier	Adjusted P-value	Enriched Genes
Cluster 2
respiratory electron transport chain	GO:0022904	4.94E-06	Atp5b Ndufb6 Ndufb11 Atp5e Ndufs4 Etfb Sdhd Ndufv2
electron transport chain	GO:0022900	4.94E-06	Atp5b Ndufb6 Ndufb11 Atp5e Ndufs4 Etfb Sdhd Ndufv2
mitochondrial transport	GO:0006839	5.37E-05	Chchd4 Atp5b Atp5e Timm22 Mrpl12 Bid Tomm5
energy coupled proton transport, down electro-chemical gradient	GO:0015985	5.83E-03	Atp5b Atp5e Atp5g3
ATP synthesis coupled proton transport	GO:0015986	5.83E-03	Atp5b Atp5e Atp5g3
mitochondrial membrane part	GO:0044455	9.60E-08	Atp5b Ndufb6 Ndufb11 Atp5e Ndufs4 Atp5g3 Sdhd Ndufv2 Bid Tomm5
mitochondrion	GO:0005739	2.74E-06	Oxnad1 Uqcc2 Bola1 Mrpl27 Mrpl14 Etfb Sdhd Mrpl12 Chchd4 Nt5c Mrpl41 Atp5b Fdx1 Ndufs4 Suclg1 Ndufv2 Bid Tomm5 Ccdc51 Tmem14c
mitochondrial membrane	GO:0031966	3.82E-05	Atp5b Ndufb6 Ndufb11 Uqcc2 Ndufs4 Suclg1 Timm22 Sdhd Ndufv2 Bid Mrpl12
mitochondrial matrix	GO:0005759	3.82E-05	Atp5b Dtymk Uqcc2 Atp5e Fdx1 Suclg1 Etfb Fdx1l
organellar large ribosomal subunit	GO:0000315	3.33E-04	Mrpl41 Mrpl27 Mrpl12
Cluster 3
positive regulation of gene expression, epigenetic	GO:0045815	8.87E-03	Kmt2b Padi2 Arid1a
chromatin modification	GO:0016568	2.15E-03	Rere Kmt2d Crebbp Kdm2b Sap130 Tet3 Kmt2b Padi2 Arid1a Bcorl1
histone H3-K4 methylation	GO:0051568	1.21E-02	Kmt2d Kmt2b Tet3
histone modification	GO:0016570	8.87E-03	Kmt2d Crebbp Kdm2b Kmt2b Sap130 Tet3 Padi2
covalent chromatin modification	GO:0016569	8.87E-03	Kmt2d Crebbp Kdm2b Kmt2b Sap130 Tet3 Padi2
E2f2 LOF in MMTV-myc mouse, down	GDS4094	4.24E-03	Ncor2 Zfhx3 Crebbp Creb3l2 Wasl Luc7l2
Delta-Notch Signaling Pathway Mus musculus	WP265	8.97E-03	Ncor2 Notch1 Furin Zfpm1
Notch Signaling Pathway Mus musculus	WP29	1.01E-02	Ncor2 Crebbp Notch1