@prefix this: <http://www.tkuhn.ch/bel2nanopub/RAgAZGmKKw_vwJnyN4xbpVE2idhPjnZCtN_yA_5fQKots> .
@prefix sub: <http://www.tkuhn.ch/bel2nanopub/RAgAZGmKKw_vwJnyN4xbpVE2idhPjnZCtN_yA_5fQKots#> .
@prefix beldoc: <http://resource.belframework.org/belframework/20131211/knowledge/large_corpus.bel> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix dce: <http://purl.org/dc/elements/1.1/> .
@prefix pav: <http://purl.org/pav/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix belv: <http://www.selventa.com/vocabulary/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix go: <http://amigo.geneontology.org/amigo/term/GO:> .
@prefix Protein: <http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI_36080> .
@prefix mgi: <http://www.informatics.jax.org/marker/MGI:> .
@prefix geneProductOf: <http://purl.obolibrary.org/obo/RO_0002204> .
@prefix hasAgent: <http://semanticscience.org/resource/SIO_000139> .
@prefix RNA: <http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI_33697> .
@prefix species: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=> .
@prefix occursIn: <http://purl.obolibrary.org/obo/BFO_0000066> .
@prefix pubmed: <http://www.ncbi.nlm.nih.gov/pubmed/> .
@prefix orcid: <http://orcid.org/> .

sub:Head {
  this: np:hasAssertion sub:assertion;
    np:hasProvenance sub:provenance;
    np:hasPublicationInfo sub:pubinfo;
    a np:Nanopublication .
}

sub:assertion {
  sub:_1 hasAgent: sub:_2;
    a go:0042789 .
  
  sub:_2 geneProductOf: mgi:96173;
    a Protein: .
  
  sub:_3 geneProductOf: mgi:1347470;
    a RNA: .
  
  sub:_4 occursIn: species:10090;
    rdf:object sub:_3;
    rdf:predicate belv:directlyIncreases;
    rdf:subject sub:_1;
    a rdf:Statement .
  
  sub:assertion rdfs:label "tscript(p(MGI:Hoxa13)) => r(MGI:Foxf1)" .
}

sub:provenance {
  beldoc: dce:description "Approximately 61,000 statements.";
    dce:rights "Copyright (c) 2011-2012, Selventa. All rights reserved.";
    dce:title "BEL Framework Large Corpus Document";
    pav:authoredBy sub:_6;
    pav:version "20131211" .
  
  sub:_5 prov:value "Sequence analysis of the immunoprecipitated Tie2 and Foxf1 promoter regions confirmed the presence of several of the recently identified HOXA13 binding sites (Figure 10B) [71]. Next, using an electrophoretic mobility shift assay (EMSA), the HOXA13 DNA binding domain was confirmed to bind the promoter regions detected by the ChIP assay in a concentration-dependent manner (Figure 10C). Quantitation of HOXA13's affinity for the Tie2 and Foxf1 ChIP-positive regions using fluorescence polarization anisotropy revealed high affinity for the binding sites present in Tie2 (Kd = 27±1.4 nM and 22 nM±1.6 nM) and Foxf1 (Kd = 48±4 nM) compared to a control sequence lacking the HOXA13 binding site (Kd = 250±22 nM) (Figure 10D and 10E).  Next, the capacity of HOXA13 to regulate gene expression through the 140 base-pair Tie2 and 121 base-pair Foxf1 ChIP-positive DNA fragments was examined (Figure 10F). The pGL3-Basic vector was selected for this analysis based on previous studies that confirm its capacity to assess promoter/enhancer activity in vitro, including previous characterizations of HOXA13's capacity to regulate transcription from minimal promoter elements [72], [74]–[78]. In the absence of the Tie2 or Foxf1 DNA elements, the empty pGL3-basic luciferase plasmid exhibited only a minor increase in luciferase expression when co-transfected with a Hoxa13 expression plasmid (Figure 10F). Similarly, the same luciferase vector containing either the Tie2 or the Foxf1 ChIP-positive regions also exhibited minimal luciferase expression in the absence of HOXA13 (Figure 10F). Co-transfection with a Hoxa13 expression vector stimulated luciferase expression from these minimal promoter elements resulting in low but significant increases in normalized luciferase expression: 3.7 fold for Tie2 and 3.2 fold for Foxf1";
    prov:wasQuotedFrom pubmed:18483557 .
  
  sub:_6 rdfs:label "Selventa" .
  
  sub:assertion prov:hadPrimarySource pubmed:18483557;
    prov:wasDerivedFrom beldoc:, sub:_5 .
}

sub:pubinfo {
  this: dct:created "2014-07-03T14:33:21.351+02:00"^^xsd:dateTime;
    pav:createdBy orcid:0000-0001-6818-334X, orcid:0000-0002-1267-0234 .
}