Table 4 Functional Pathways in Highly Connected Pluripotency and Differentiation Related Genes in the Zhou et al Network

9.72E-17

er-golgi transport; protein localization; protein transport; vesicle-mediated transport; secretion by cell; cellular localization; secretory pathway; intracellular transport;

Myl6 (0.994), Sh3glb1 (0.993), Tm9sf3 (0.993), Tram1 (0.992), Derl1 (0.991), Serinc1 (0.991), Lman1 (0.991), Lrp10 (0.991), Mcfd2 (0.99), Mcfd2 (0.99), Tmed10 (0.99), Tpcn1 (0.989), Arl1 (0.989), Tinagl (0.987), Rab2 (0.987), Txndc1 (0.987), Col4a1 (0.987)

5.65E-08

Glycan structures – biosynthesis 1; signal-anchor; transferase activity, glycosyltransferase

Glt8d1 (0.993), Creb3 (0.991), Fut8 (0.99), Fkrp (0.99), Extl2 (0.989), Glt8d3 (0.987), Itm2c (0.986), Hs3st1 (0.986), Pofut2 (0.986), Dpagt1 (0.985), Mgat2 (0.983), Abhd6 (0.982), Ddost (0.982), Ndst2 (0.981), B4galnt1 (0.981), St3gal6 (0.98)

2.98E-06

membrane; transmembrane; transmembrane region; topological domain:Cytoplasmic

H13 (0.996), Pdgfra (0.994), Cd59a (0.994), Glt8d1 (0.993), Sh3glb1 (0.993), Tm9sf3 (0.993), Tram1 (0.992), Gdpd5 (0.991)

0.00185

organ development; system development; anatomical structure morphogenesis; cell differentiation; organ morphogenesis

Pdgfra (0.994), Myl6 (0.994), Sh3glb1 (0.993), Lmo4 (0.992), Rgnef (0.989), Syvn1 (0.988), Kit (0.988), Fndc3b (0.988), Txndc1 (0.987), Lama1 (0.987), Barx1 (0.986), Col4a2 (0.986), Ctgf (0.985), Fgf3 (0.985), Crim1 (0.983), Pthr1 (0.983)

p-value

Functional Groups

Black Module highly connected genes (kME)

1.98E-08

response to DNA damage stimulus; DNA damage; DNA repair

Msh6 (0.993), Rif1 (0.983), Mre11a (0.982), Setx (0.974), Xrcc5 (0.971), Chek1 (0.968), Xab2 (0.967), Xrn2 (0.967), Trp53 (0.959), Npm1 (0.958), Tdp1 (0.955), Bccip (0.954)

3.75E-08

Mitochondrion; transit peptide; Mitochondrion

Mrpl15 (0.992), Ppif (0.991), Mrps5 (0.987), Hspa9 (0.984), Coq3 (0.984), Tst (0.981), Mrpl45 (0.98), Akap1 (0.979), L2hgdh (0.978), Mrps31 (0.978), Chchd4 (0.976), Abce1 (0.975), Dci (0.975), Fpgs (0.974), Mrpl39 (0.973), Bdh1 (0.971)

5.83E-08

nucleus; biopolymer metabolic process; DNA binding; cellular metabolic process; Transcription regulation;

Msh6 (0.993), Pes1 (0.991), Zic3 (0.991), Uchl1 (0.99), Rnf138 (0.99), Rnf138 (0.99), Wdr36 (0.989), Pou5f1 (0.989), Rbpj (0.987), Glo1 (0.987), Tdgf1 (0.987), OTTMUSG00000010173 (0.986), Aarsd1 (0.986), Nup133 (0.985), Xpo1 (0.985), Xpo1 (0.985), Dnajc6 (0.985), Klhl13 (0.984), Dppa4 (0.984),

5.26E-04

cell cycle phase; cell cycle process; cell cycle; mitotic cell cycle; mitosis; cell division

Pes1 (0.991), Rif1 (0.983), Mre11a (0.982), Gtpbp4 (0.972), Chek1 (0.968), Mnat1 (0.966), Rcc2 (0.964), Gadd45gip1 (0.963), Rpa1 (0.961), Hells (0.96), Trp53 (0.959), Terf1 (0.959)