title: Network based transcription factor analysis of regenerating axolotl limbs.
abstract: BACKGROUND
  Studies on amphibian limb regeneration began in the early 1700's but we still do not completely understand the cellular and molecular events of this unique process. Understanding a complex biological process such as limb regeneration is more complicated than the knowledge of the individual genes or proteins involved. Here we followed a systems biology approach in an effort to construct the networks and pathways of protein interactions involved in formation of the accumulation blastema in regenerating axolotl limbs.
  
  
  RESULTS
  We used the human orthologs of proteins previously identified by our research team as bait to identify the transcription factor (TF) pathways and networks that regulate blastema formation in amputated axolotl limbs. The five most connected factors, c-Myc, SP1, HNF4A, ESR1 and p53 regulate ~50% of the proteins in our data. Among these, c-Myc and SP1 regulate 36.2% of the proteins. c-Myc was the most highly connected TF (71 targets). Network analysis showed that TGF-β1 and fibronectin (FN) lead to the activation of these TFs. We found that other TFs known to be involved in epigenetic reprogramming, such as Klf4, Oct4, and Lin28 are also connected to c-Myc and SP1.
  
  
  CONCLUSIONS
  Our study provides a systems biology approach to how different molecular entities inter-connect with each other during the formation of an accumulation blastema in regenerating axolotl limbs. This approach provides an in silico methodology to identify proteins that are not detected by experimental methods such as proteomics but are potentially important to blastema formation. We found that the TFs, c-Myc and SP1 and their target genes could potentially play a central role in limb regeneration. Systems biology has the potential to map out numerous other pathways that are crucial to blastema formation in regeneration-competent limbs, to compare these to the pathways that characterize regeneration-deficient limbs and finally, to identify stem cell markers in regeneration.
authors.affiliation: School of Informatics, Indiana University-Purdue University Indianapolis, IN 46202, USA.
authors.forename: Deepali
authors.initials: D
authors.lastname: Jhamb
authors.forename: Nandini
authors.initials: N
authors.lastname: Rao
authors.forename: Derek J
authors.initials: DJ
authors.lastname: Milner
authors.forename: Fengyu
authors.initials: F
authors.lastname: Song
authors.forename: Jo Ann
authors.initials: JA
authors.lastname: Cameron
authors.forename: David L
authors.initials: DL
authors.lastname: Stocum
authors.forename: Mathew J
authors.initials: MJ
authors.lastname: Palakal
mesh_terms: D000558:Ambystoma mexicanum / Q000235:genetics / Q000502:physiology; D000818:Animals; D018076:DNA, Complementary / Q000235:genetics; D005121:Extremities / Q000502:physiology*; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D000090062:Kruppel-Like Factor 4; D040901:Proteomics; D012038:Regeneration / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*; D053773:Transforming Growth Factor beta1 / Q000235:genetics
chemical_list: D018076:DNA, Complementary; C000715467:KLF4 protein, human; D000090062:Kruppel-Like Factor 4; D014157:Transcription Factors; D053773:Transforming Growth Factor beta1