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

From: Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells

p-value Functional Groups Blue Module highly connected genes (kME)
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)
  1. Enriched GO terms of genes with the highest 5% black and blue k ME 's. Highly connected genes in each functional group are given. All k ME values are highly significant (Bonferroni corrected p-value < 0.00015).