<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Document definition -->
<!DOCTYPE gomo[
	<!ELEMENT gomo (program, motif*)>
	<!ATTLIST gomo xmlns:xsi CDATA #IMPLIED
			 version CDATA #REQUIRED
			 release CDATA #REQUIRED
			>
		<!ELEMENT program (gomapfile, seqscorefile*)>
		<!ATTLIST program
				 name CDATA #REQUIRED
				 cmd CDATA #REQUIRED
				 gene_url CDATA #IMPLIED
				 outdir CDATA #REQUIRED
				 clobber CDATA #REQUIRED
				 text_only CDATA #REQUIRED
				 use_e_values CDATA #REQUIRED
				 score_e_thresh CDATA #REQUIRED
				 min_gene_count CDATA #REQUIRED
				 motifs CDATA #IMPLIED
				 shuffle_scores CDATA #REQUIRED
				 q_threshold CDATA #REQUIRED
				>
			<!ELEMENT gomapfile EMPTY>
			<!ATTLIST gomapfile path CDATA #REQUIRED >
			<!ELEMENT seqscorefile EMPTY>
			<!ATTLIST seqscorefile path CDATA #REQUIRED >
		<!ELEMENT motif (goterm*)>
		<!ATTLIST motif
				 id CDATA #REQUIRED
				 genecount CDATA #REQUIRED
				 logo CDATA #IMPLIED
				>
			<!ELEMENT goterm (gene*)>
			<!ATTLIST goterm
					 id CDATA #REQUIRED
					 score CDATA #REQUIRED
					 pvalue CDATA #REQUIRED
					 qvalue CDATA #REQUIRED
					 annotated CDATA #REQUIRED
					 group CDATA #REQUIRED
					 nabove CDATA #REQUIRED
					 nbelow CDATA #REQUIRED
					 implied (u|y|n) #REQUIRED
					 name CDATA #REQUIRED
					>
				<!ELEMENT gene EMPTY>
				<!ATTLIST gene
						 id CDATA #REQUIRED
						 rank CDATA #REQUIRED
						>
]>
<gomo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="4.10.0" release="Wed May 21 10:35:36 2014 +1000">
	<program name="gomo"
			 seed="3993088087"
			 cmd="gomo --oc gomo_example_output_files --dag go.dag --images . bacteria_escherichia_coli_k12_1000_199.na.csv ama.xml"
			 gene_url="http://regulondb.ccg.unam.mx/SearchListController?object_form=GN&amp;object_id=!!GENEID!!&amp;key_id_org=ECK12&amp;Submit=Go"
			 outdir="gomo_example_output_files" clobber="TRUE" text_only="FALSE"
			 use_e_values="TRUE" score_e_thresh="0"
			 min_gene_count="1"
			 shuffle_scores="1000" q_threshold="0.05"
			>
		<gomapfile path="bacteria_escherichia_coli_k12_1000_199.na.csv" />
		<seqscorefile path="ama.xml" />
	</program>
	<motif id="crp" genecount="2518" logo="logocrp.png">
		<goterm id="GO:0009056" score="8.869e-07" pvalue="5.615e-07" qvalue="4.550e-04" annotated="59" group="b" nabove="2" nbelow="1073" implied="y"
				name="catabolic process">
			<gene id="deoC" rank="24" />
			<gene id="iraP" rank="31" />
			<gene id="fucA" rank="51" />
			<gene id="fucP" rank="52" />
			<gene id="exuT" rank="64" />
			<gene id="uxaC" rank="65" />
			<gene id="tdcA" rank="71" />
			<gene id="rhaB" rank="80" />
			<gene id="araB" rank="143" />
			<gene id="fruB" rank="147" />
		</goterm>
		<goterm id="GO:0044248" score="1.341e-06" pvalue="5.615e-07" qvalue="4.550e-04" annotated="52" group="b" nabove="5" nbelow="852" implied="y"
				name="cellular catabolic process">
			<gene id="deoC" rank="24" />
			<gene id="fucA" rank="51" />
			<gene id="fucP" rank="52" />
			<gene id="exuT" rank="64" />
			<gene id="uxaC" rank="65" />
			<gene id="tdcA" rank="71" />
			<gene id="rhaB" rank="80" />
			<gene id="araB" rank="143" />
			<gene id="fruB" rank="147" />
			<gene id="fruB" rank="148" />
		</goterm>
		<goterm id="GO:0008643" score="1.075e-04" pvalue="8.422e-06" qvalue="4.550e-03" annotated="7" group="b" nabove="4" nbelow="93" implied="n"
				name="carbohydrate transport">
			<gene id="fucP" rank="52" />
			<gene id="malE" rank="135" />
			<gene id="malK" rank="136" />
			<gene id="ulaA" rank="172" />
			<gene id="xylF" rank="177" />
			<gene id="idnD" rank="196" />
			<gene id="yjjL" rank="840" />
		</goterm>
		<goterm id="GO:0051119" score="2.285e-04" pvalue="2.077e-05" qvalue="7.583e-03" annotated="5" group="m" nabove="6" nbelow="113" implied="n"
				name="sugar transmembrane transporter activity">
			<gene id="fucP" rank="52" />
			<gene id="glpT" rank="99" />
			<gene id="malE" rank="135" />
			<gene id="malK" rank="136" />
			<gene id="xylF" rank="177" />
		</goterm>
		<goterm id="GO:0044275" score="2.652e-04" pvalue="2.695e-05" qvalue="7.583e-03" annotated="20" group="b" nabove="9" nbelow="124" implied="n"
				name="cellular carbohydrate catabolic process">
			<gene id="fucA" rank="51" />
			<gene id="fucP" rank="52" />
			<gene id="rhaB" rank="80" />
			<gene id="araB" rank="143" />
			<gene id="fruB" rank="147" />
			<gene id="fruB" rank="148" />
			<gene id="nagB" rank="153" />
			<gene id="xylA" rank="176" />
			<gene id="idnD" rank="196" />
			<gene id="nanA" rank="204" />
		</goterm>
		<goterm id="GO:0015144" score="2.665e-04" pvalue="2.807e-05" qvalue="7.583e-03" annotated="7" group="m" nabove="5" nbelow="157" implied="y"
				name="carbohydrate transmembrane transporter activity">
			<gene id="fucP" rank="52" />
			<gene id="glpT" rank="99" />
			<gene id="malE" rank="135" />
			<gene id="malK" rank="136" />
			<gene id="ulaA" rank="172" />
			<gene id="xylF" rank="177" />
			<gene id="ycaI" rank="1391" />
		</goterm>
		<goterm id="GO:0016861" score="3.954e-04" pvalue="4.604e-05" qvalue="1.058e-02" annotated="13" group="m" nabove="4" nbelow="25" implied="n"
				name="intramolecular oxidoreductase activity, interconverting aldoses and ketoses">
			<gene id="fucP" rank="52" />
			<gene id="uxaC" rank="65" />
			<gene id="rhaB" rank="80" />
			<gene id="srlA" rank="111" />
			<gene id="araB" rank="143" />
			<gene id="nagB" rank="153" />
			<gene id="xylA" rank="176" />
			<gene id="hisL" rank="637" />
			<gene id="yihU" rank="858" />
			<gene id="rpiB" rank="895" />
		</goterm>
		<goterm id="GO:0016860" score="4.737e-04" pvalue="5.222e-05" qvalue="1.058e-02" annotated="14" group="m" nabove="3" nbelow="70" implied="y"
				name="intramolecular oxidoreductase activity">
			<gene id="fucP" rank="52" />
			<gene id="uxaC" rank="65" />
			<gene id="rhaB" rank="80" />
			<gene id="srlA" rank="111" />
			<gene id="araB" rank="143" />
			<gene id="nagB" rank="153" />
			<gene id="xylA" rank="176" />
			<gene id="hisL" rank="637" />
			<gene id="yihU" rank="858" />
			<gene id="rpiB" rank="895" />
		</goterm>
		<goterm id="GO:0016052" score="5.421e-04" pvalue="6.176e-05" qvalue="1.112e-02" annotated="24" group="b" nabove="5" nbelow="182" implied="y"
				name="carbohydrate catabolic process">
			<gene id="fucA" rank="51" />
			<gene id="fucP" rank="52" />
			<gene id="rhaB" rank="80" />
			<gene id="araB" rank="143" />
			<gene id="fruB" rank="147" />
			<gene id="fruB" rank="148" />
			<gene id="nagB" rank="153" />
			<gene id="ybjQ" rank="159" />
			<gene id="xylA" rank="176" />
			<gene id="idnD" rank="196" />
		</goterm>
		<goterm id="GO:0009057" score="5.850e-04" pvalue="6.962e-05" qvalue="1.128e-02" annotated="30" group="b" nabove="4" nbelow="215" implied="y"
				name="macromolecule catabolic process">
			<gene id="iraP" rank="31" />
			<gene id="fucA" rank="51" />
			<gene id="fucP" rank="52" />
			<gene id="rhaB" rank="80" />
			<gene id="araB" rank="143" />
			<gene id="fruB" rank="147" />
			<gene id="fruB" rank="148" />
			<gene id="nagB" rank="153" />
			<gene id="ybjQ" rank="159" />
			<gene id="xylA" rank="176" />
		</goterm>
		<goterm id="GO:0016853" score="7.322e-04" pvalue="9.321e-05" qvalue="1.373e-02" annotated="37" group="m" nabove="2" nbelow="232" implied="y"
				name="isomerase activity">
			<gene id="fucP" rank="52" />
			<gene id="uxaC" rank="65" />
			<gene id="yqcC" rank="78" />
			<gene id="rhaB" rank="80" />
			<gene id="srlA" rank="111" />
			<gene id="araB" rank="143" />
			<gene id="nagB" rank="153" />
			<gene id="xylA" rank="176" />
			<gene id="nanA" rank="204" />
			<gene id="nanC" rank="238" />
		</goterm>
		<goterm id="GO:0044265" score="8.893e-04" pvalue="1.157e-04" qvalue="1.562e-02" annotated="23" group="b" nabove="9" nbelow="133" implied="n"
				name="cellular macromolecule catabolic process">
			<gene id="fucA" rank="51" />
			<gene id="fucP" rank="52" />
			<gene id="rhaB" rank="80" />
			<gene id="araB" rank="143" />
			<gene id="fruB" rank="147" />
			<gene id="fruB" rank="148" />
			<gene id="nagB" rank="153" />
			<gene id="xylA" rank="176" />
			<gene id="idnD" rank="196" />
			<gene id="nanA" rank="204" />
		</goterm>
		<goterm id="GO:0019321" score="1.272e-03" pvalue="1.752e-04" qvalue="2.184e-02" annotated="8" group="b" nabove="10" nbelow="53" implied="n"
				name="pentose metabolic process">
			<gene id="fucA" rank="51" />
			<gene id="fucP" rank="52" />
			<gene id="rhaB" rank="80" />
			<gene id="araB" rank="143" />
			<gene id="xylA" rank="176" />
			<gene id="rbsD" rank="365" />
			<gene id="aldA" rank="1059" />
			<gene id="yiaK" rank="1950" />
		</goterm>
	</motif>
	<motif id="nagC" genecount="2518" logo="logonagC.png">
		<goterm id="GO:0051704" score="1.801e-04" pvalue="2.190e-05" qvalue="2.269e-02" annotated="13" group="b" nabove="1" nbelow="1141" implied="y"
				name="multi-organism process">
			<gene id="srlA" rank="79" />
			<gene id="solA" rank="182" />
			<gene id="yjbE" rank="305" />
			<gene id="bhsA" rank="374" />
			<gene id="ymgC" rank="388" />
			<gene id="dcuB" rank="442" />
			<gene id="yihR" rank="478" />
			<gene id="hlyE" rank="535" />
			<gene id="ttdA" rank="589" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0042710" score="4.020e-04" pvalue="5.278e-05" qvalue="2.269e-02" annotated="11" group="b" nabove="2" nbelow="11" implied="n"
				name="biofilm formation">
			<gene id="srlA" rank="79" />
			<gene id="solA" rank="182" />
			<gene id="yjbE" rank="305" />
			<gene id="bhsA" rank="374" />
			<gene id="ymgC" rank="388" />
			<gene id="dcuB" rank="442" />
			<gene id="yihR" rank="478" />
			<gene id="ttdA" rank="589" />
			<gene id="ymgA" rank="822" />
			<gene id="yjiP" rank="893" />
		</goterm>
		<goterm id="GO:0007047" score="8.308e-04" pvalue="1.089e-04" qvalue="2.269e-02" annotated="5" group="b" nabove="7" nbelow="12" implied="y"
				name="cellular cell wall organization">
			<gene id="mltB" rank="78" />
			<gene id="mltA" rank="98" />
			<gene id="mipA" rank="129" />
			<gene id="mraZ" rank="166" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0009252" score="8.308e-04" pvalue="1.089e-04" qvalue="2.269e-02" annotated="5" group="b" nabove="31" nbelow="4" implied="n"
				name="peptidoglycan biosynthetic process">
			<gene id="mltB" rank="78" />
			<gene id="mltA" rank="98" />
			<gene id="mipA" rank="129" />
			<gene id="mraZ" rank="166" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0009273" score="8.308e-04" pvalue="1.089e-04" qvalue="2.269e-02" annotated="5" group="b" nabove="6" nbelow="15" implied="y"
				name="peptidoglycan-based cell wall biogenesis">
			<gene id="mltB" rank="78" />
			<gene id="mltA" rank="98" />
			<gene id="mipA" rank="129" />
			<gene id="mraZ" rank="166" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0031504" score="8.308e-04" pvalue="1.089e-04" qvalue="2.269e-02" annotated="5" group="b" nabove="8" nbelow="0" implied="n"
				name="peptidoglycan-based cell wall organization">
			<gene id="mltB" rank="78" />
			<gene id="mltA" rank="98" />
			<gene id="mipA" rank="129" />
			<gene id="mraZ" rank="166" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0042546" score="8.308e-04" pvalue="1.089e-04" qvalue="2.269e-02" annotated="5" group="b" nabove="5" nbelow="59" implied="y"
				name="cell wall biogenesis">
			<gene id="mltB" rank="78" />
			<gene id="mltA" rank="98" />
			<gene id="mipA" rank="129" />
			<gene id="mraZ" rank="166" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0004553" score="1.101e-03" pvalue="1.617e-04" qvalue="2.620e-02" annotated="5" group="m" nabove="4" nbelow="163" implied="n"
				name="hydrolase activity, hydrolyzing O-glycosyl compounds">
			<gene id="chiA" rank="11" />
			<gene id="uidA" rank="94" />
			<gene id="mltA" rank="98" />
			<gene id="essD" rank="384" />
		</goterm>
		<goterm id="GO:0016798" score="1.101e-03" pvalue="1.617e-04" qvalue="2.620e-02" annotated="5" group="m" nabove="3" nbelow="215" implied="y"
				name="hydrolase activity, acting on glycosyl bonds">
			<gene id="chiA" rank="11" />
			<gene id="uidA" rank="94" />
			<gene id="mltA" rank="98" />
			<gene id="essD" rank="384" />
		</goterm>
	</motif>
	<motif id="narP" genecount="2518" logo="logonarP.png">
		<goterm id="GO:0009061" score="3.737e-04" pvalue="5.446e-05" qvalue="4.021e-02" annotated="11" group="b" nabove="7" nbelow="6" implied="n"
				name="anaerobic respiration">
			<gene id="fdnG" rank="3" />
			<gene id="nirB" rank="9" />
			<gene id="narG" rank="21" />
			<gene id="frdA" rank="25" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="lldP" rank="716" />
			<gene id="narZ" rank="797" />
			<gene id="zwf" rank="2161" />
		</goterm>
		<goterm id="GO:0045333" score="5.182e-04" pvalue="7.580e-05" qvalue="4.021e-02" annotated="15" group="b" nabove="6" nbelow="34" implied="y"
				name="cellular respiration">
			<gene id="fdnG" rank="3" />
			<gene id="nirB" rank="9" />
			<gene id="narG" rank="21" />
			<gene id="frdA" rank="25" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="sdhC" rank="674" />
			<gene id="lldP" rank="716" />
			<gene id="narZ" rank="797" />
			<gene id="cyoA" rank="980" />
		</goterm>
		<goterm id="GO:0030151" score="6.633e-04" pvalue="9.938e-05" qvalue="4.021e-02" annotated="5" group="m" nabove="6" nbelow="0" implied="n"
				name="molybdenum ion binding">
			<gene id="fdnG" rank="3" />
			<gene id="narG" rank="21" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="narZ" rank="797" />
		</goterm>
		<goterm id="GO:0006091" score="9.717e-04" pvalue="1.454e-04" qvalue="4.021e-02" annotated="16" group="b" nabove="4" nbelow="102" implied="y"
				name="generation of precursor metabolites and energy">
			<gene id="fdnG" rank="3" />
			<gene id="nirB" rank="9" />
			<gene id="narG" rank="21" />
			<gene id="frdA" rank="25" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="sdhC" rank="674" />
			<gene id="lldP" rank="716" />
			<gene id="narZ" rank="797" />
			<gene id="cyoA" rank="980" />
		</goterm>
		<goterm id="GO:0015980" score="9.717e-04" pvalue="1.454e-04" qvalue="4.021e-02" annotated="16" group="b" nabove="5" nbelow="75" implied="y"
				name="energy derivation by oxidation of organic compounds">
			<gene id="fdnG" rank="3" />
			<gene id="nirB" rank="9" />
			<gene id="narG" rank="21" />
			<gene id="frdA" rank="25" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="sdhC" rank="674" />
			<gene id="lldP" rank="716" />
			<gene id="narZ" rank="797" />
			<gene id="cyoA" rank="980" />
		</goterm>
		<goterm id="GO:0017004" score="1.063e-03" pvalue="1.623e-04" qvalue="4.021e-02" annotated="5" group="b" nabove="12" nbelow="14" implied="n"
				name="cytochrome complex assembly">
			<gene id="napF" rank="2" />
			<gene id="fdnG" rank="3" />
			<gene id="narG" rank="21" />
			<gene id="cydA" rank="607" />
			<gene id="sdhC" rank="674" />
		</goterm>
		<goterm id="GO:0043623" score="1.063e-03" pvalue="1.623e-04" qvalue="4.021e-02" annotated="5" group="b" nabove="11" nbelow="105" implied="y"
				name="cellular protein complex assembly">
			<gene id="napF" rank="2" />
			<gene id="fdnG" rank="3" />
			<gene id="narG" rank="21" />
			<gene id="cydA" rank="607" />
			<gene id="sdhC" rank="674" />
		</goterm>
		<goterm id="GO:0019725" score="1.382e-03" pvalue="2.442e-04" qvalue="4.237e-02" annotated="13" group="b" nabove="5" nbelow="131" implied="n"
				name="cellular homeostasis">
			<gene id="aqpZ" rank="27" />
			<gene id="nhaB" rank="30" />
			<gene id="adiC" rank="60" />
			<gene id="gadB" rank="77" />
			<gene id="mscS" rank="156" />
			<gene id="gadA" rank="252" />
			<gene id="adiA" rank="363" />
			<gene id="nhaA" rank="533" />
			<gene id="kefA" rank="566" />
			<gene id="mscL" rank="823" />
		</goterm>
		<goterm id="GO:0042592" score="1.382e-03" pvalue="2.442e-04" qvalue="4.237e-02" annotated="13" group="b" nabove="3" nbelow="275" implied="y"
				name="homeostatic process">
			<gene id="aqpZ" rank="27" />
			<gene id="nhaB" rank="30" />
			<gene id="adiC" rank="60" />
			<gene id="gadB" rank="77" />
			<gene id="mscS" rank="156" />
			<gene id="gadA" rank="252" />
			<gene id="adiA" rank="363" />
			<gene id="nhaA" rank="533" />
			<gene id="kefA" rank="566" />
			<gene id="mscL" rank="823" />
		</goterm>
		<goterm id="GO:0048878" score="1.382e-03" pvalue="2.442e-04" qvalue="4.237e-02" annotated="13" group="b" nabove="4" nbelow="188" implied="n"
				name="chemical homeostasis">
			<gene id="aqpZ" rank="27" />
			<gene id="nhaB" rank="30" />
			<gene id="adiC" rank="60" />
			<gene id="gadB" rank="77" />
			<gene id="mscS" rank="156" />
			<gene id="gadA" rank="252" />
			<gene id="adiA" rank="363" />
			<gene id="nhaA" rank="533" />
			<gene id="kefA" rank="566" />
			<gene id="mscL" rank="823" />
		</goterm>
		<goterm id="GO:0009055" score="1.539e-03" pvalue="2.858e-04" qvalue="4.507e-02" annotated="14" group="m" nabove="1" nbelow="7" implied="n"
				name="electron carrier activity">
			<gene id="fdnG" rank="3" />
			<gene id="narG" rank="21" />
			<gene id="frdA" rank="25" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="cydA" rank="607" />
			<gene id="sdhC" rank="674" />
			<gene id="narZ" rank="797" />
			<gene id="cyoA" rank="980" />
			<gene id="ndh" rank="1014" />
		</goterm>
		<goterm id="GO:0065007" score="1.695e-03" pvalue="3.273e-04" qvalue="4.732e-02" annotated="46" group="b" nabove="1" nbelow="6719" implied="y"
				name="biological regulation">
			<gene id="napF" rank="2" />
			<gene id="aqpZ" rank="27" />
			<gene id="nhaB" rank="30" />
			<gene id="adiC" rank="60" />
			<gene id="gadB" rank="77" />
			<gene id="acnA" rank="106" />
			<gene id="lptA" rank="145" />
			<gene id="mscS" rank="156" />
			<gene id="sohA" rank="226" />
			<gene id="alaS" rank="236" />
		</goterm>
		<goterm id="GO:0065008" score="1.839e-03" pvalue="3.734e-04" qvalue="4.982e-02" annotated="15" group="b" nabove="2" nbelow="1381" implied="y"
				name="regulation of biological quality">
			<gene id="aqpZ" rank="27" />
			<gene id="nhaB" rank="30" />
			<gene id="adiC" rank="60" />
			<gene id="gadB" rank="77" />
			<gene id="mscS" rank="156" />
			<gene id="sohA" rank="226" />
			<gene id="gadA" rank="252" />
			<gene id="adiA" rank="363" />
			<gene id="nhaA" rank="533" />
			<gene id="kefA" rank="566" />
		</goterm>
	</motif>
</gomo>
