<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pazar SYSTEM "http://www.pazar.info/pazar.dtd">
<pazar>
  <project edit_date="13-12-05" pazar_id="p_0001"
    project_name="example_project3" status="restricted">
    <user affiliation="CMMT" first_name="first_name"
      last_name="last_name" pazar_id="u_0001" username="cmmt_user"/>
  </project>
  <data>
    <gene_source db_accn="ENSG00000133256" description="PDE6B" pazar_id="gs_0001">
      <db_source db_name="EnsEMBL" assembly="NCBI 35"/>
      <tsr fuzzy_end="609373" fuzzy_start="609373" pazar_id="tsr_0001">
        <transcript db_accn="ENST00000255622" pazar_id="tr_0001">
          <db_source db_name="EnsEMBL" assembly="NCBI 35"/>
      	</transcript>
        <reg_seq pazar_id="rs_0001" quality="tested" sequence="gagtgagtcagctgacccgcccccggggttcctaatctcactaagaaagactttgctgatgacagggtttcctgggagtccatgcgtgcctggagcagcagcgtctccagggacaggcagccacc">
          <coordinate begin="609291" end="609415" length="125" strand="+">
            <location band="p16.3" chr="4" species="Homo sapiens">
              <db_source db_name="EnsEMBL" assembly="NCBI 35"/>
            </location>
          </coordinate>
        </reg_seq>
        <reg_seq pazar_id="rs_0002" quality="tested" sequence="gttcctaatctcactaagaaagactttgctgatgacagggtttcctgggagtccatgcgtgcctggagcagcagcgtctccagggacaggcagccacc">
          <coordinate begin="609318" end="609415" length="98" strand="+">
            <location band="p16.3" chr="4" species="Homo sapiens">
              <db_source db_name="EnsEMBL" assembly="NCBI 35"/>
            </location>
          </coordinate>
        </reg_seq>
      </tsr>
    </gene_source>
    <gene_source db_accn="ENSG00000105392" description="CRX" pazar_id="gs_0002">
      <db_source db_name="EnsEMBL" assembly="NCBI 35"/>
      <transcript db_accn="ENST00000221996" pazar_id="tr_0002">
        <db_source db_name="EnsEMBL" assembly="NCBI 35"/>
        <tf class="Homeobox" pazar_id="tf_0001"/>
      </transcript>
    </gene_source>
    <funct_tf funct_tf_name="CRX" pazar_id="fu_0001">
      <tf_unit pazar_id="tu_0001" tf_id="tf_0001"/>
    </funct_tf> 
    <expression pazar_id="ex_0001" quantitative="100" scale="percent"/>
    <expression pazar_id="ex_0002" quantitative="23" scale="percent"/>
    <expression pazar_id="ex_0003" quantitative="420" scale="percent"/>
    <expression pazar_id="ex_0004" quantitative="50" scale="percent"/>
    <cell name="Y79" pazar_id="ce_0001" species="Homo sapiens" status="cell__line"/>
    <cell name="embryonic head" tissue_ontology="head" description="ex vivo dissected xenopus embryonic heads" pazar_id="ce_0002" species="Xenopus tropicalis" status="primary"/>
    <time range_start="24" range_end="28" pazar_id="ti_0001" scale="stages of embryogenesis"/>
    <condition pazar_id="cd_0001" cond_type="coexpression" molecule="transcription factor" concentration="1:1" scale="ratio"/>
  </data>
  <analysis name="analysis_example3_1" cell="ce_0001">
    <evidence status_evid="provisional" type_evid="curated"/>
    <method method="luciferase gene reporter assay"/>
    <ref pmid="11943774"/>
    <input_output>
      <input inputs="rs_0001"/>
      <output outputs="ex_0001"/>
    </input_output>
    <input_output>
      <input inputs="rs_0002"/>
      <output outputs="ex_0002"/>
    </input_output>
     <input_output>
      <input inputs="rs_0001 fu_0001 cd_0001"/>
      <output outputs="ex_0003"/>
    </input_output>
    <input_output>
      <input inputs="rs_0002 fu_0001 cd_0001"/>
      <output outputs="ex_0004"/>
    </input_output>
 </analysis>
  <analysis name="analysis_example3_2" cell="ce_0002" time="ti_0001">
    <evidence status_evid="provisional" type_evid="curated"/>
    <method method="luciferase gene reporter assay"/>
    <ref pmid="11943774"/>
    <input_output>
      <input inputs="rs_0001"/>
      <output outputs="ex_0001"/>
    </input_output>
    <input_output>
      <input inputs="rs_0002"/>
      <output outputs="ex_0002"/>
    </input_output>
  </analysis>
</pazar>
