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Profiling the transcription factor regulatory networks of human cell types.

Zhang S, Tian D, Tran NH, Choi KP, Zhang L - Nucleic Acids Res. (2014)

Bottom Line: However, they have distinguishable local organizations, as suggested by the fact that wiring patterns of only a few TFs are enough to distinguish cell identities.The TF regulatory network of human embryonic stem cells (hESCs) is dense and enriched with interactions that are unseen in the networks of other cell types.The examination of specific regulatory interactions suggests that specific interactions play important roles in hESCs.

View Article: PubMed Central - PubMed

Affiliation: National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.

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(A) Proportions of hub TFs that are in Assou et al.'s list (36) and the significance of their enrichment in the ESCSN. (B) The subnetwork induced by the hub TFs in the Assou et al.'s list in the ESCSN. (C) Proportions of known hESC interactions (38) and the significance of their enrichment in the ESCSN. (D) The hESC-specific regulatory interactions appearing in a reported core transcription network for hESCs (38). (E) and (F) Two specific regulatory complex-target modules in the hESCs.
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Figure 6: (A) Proportions of hub TFs that are in Assou et al.'s list (36) and the significance of their enrichment in the ESCSN. (B) The subnetwork induced by the hub TFs in the Assou et al.'s list in the ESCSN. (C) Proportions of known hESC interactions (38) and the significance of their enrichment in the ESCSN. (D) The hESC-specific regulatory interactions appearing in a reported core transcription network for hESCs (38). (E) and (F) Two specific regulatory complex-target modules in the hESCs.

Mentions: Assou et al. (44) compiled a list of 1076 genes that are overexpressed in hESCs. In the ESCSN, the hubs are significantly enriched with the TFs encoded by the overexpressed genes in this list (P-value = 1.61e−3; hypergeometric test, Figure 6A). More interestingly, 12 of the hubs that are encoded by the genes in the list are well connected, except for ZIC2 (Figure 6B). NANOG, OTX2, PARP1, ZIC2 and ZIC3 are not hubs in the original hESC TF regulatory network.


Profiling the transcription factor regulatory networks of human cell types.

Zhang S, Tian D, Tran NH, Choi KP, Zhang L - Nucleic Acids Res. (2014)

(A) Proportions of hub TFs that are in Assou et al.'s list (36) and the significance of their enrichment in the ESCSN. (B) The subnetwork induced by the hub TFs in the Assou et al.'s list in the ESCSN. (C) Proportions of known hESC interactions (38) and the significance of their enrichment in the ESCSN. (D) The hESC-specific regulatory interactions appearing in a reported core transcription network for hESCs (38). (E) and (F) Two specific regulatory complex-target modules in the hESCs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4227771&req=5

Figure 6: (A) Proportions of hub TFs that are in Assou et al.'s list (36) and the significance of their enrichment in the ESCSN. (B) The subnetwork induced by the hub TFs in the Assou et al.'s list in the ESCSN. (C) Proportions of known hESC interactions (38) and the significance of their enrichment in the ESCSN. (D) The hESC-specific regulatory interactions appearing in a reported core transcription network for hESCs (38). (E) and (F) Two specific regulatory complex-target modules in the hESCs.
Mentions: Assou et al. (44) compiled a list of 1076 genes that are overexpressed in hESCs. In the ESCSN, the hubs are significantly enriched with the TFs encoded by the overexpressed genes in this list (P-value = 1.61e−3; hypergeometric test, Figure 6A). More interestingly, 12 of the hubs that are encoded by the genes in the list are well connected, except for ZIC2 (Figure 6B). NANOG, OTX2, PARP1, ZIC2 and ZIC3 are not hubs in the original hESC TF regulatory network.

Bottom Line: However, they have distinguishable local organizations, as suggested by the fact that wiring patterns of only a few TFs are enough to distinguish cell identities.The TF regulatory network of human embryonic stem cells (hESCs) is dense and enriched with interactions that are unseen in the networks of other cell types.The examination of specific regulatory interactions suggests that specific interactions play important roles in hESCs.

View Article: PubMed Central - PubMed

Affiliation: National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.

Show MeSH