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We can make this file beautiful and searchable if this error is corrected: It looks like row 4 should actually have 1 column, instead of 10 in line 3.
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ppgpp_regulation.tsv
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# manually curated from Ecocyc on 10/1/19: https://ecocyc.org/compound?orgid=ECOLI&id=GUANOSINE-5DP-3DP#tab=REG
# duplicate entries are not kept unless directionality differs
# some genes replaced manually with synonyms to match wcm genes (gene vs curated gene columns)
"Gene" "ppGpp" "DksA-ppGpp" "DksA" "sigma70" "sigmaS" "sigma32" "sigma54" "sigma24" "Curated Gene"
"thrL" 1 1 1 "thrL"
"thrA" 1 1 1 "thrA"
"thrB" 1 1 1 "thrB"
"thrC" 1 1 1 "thrC"
"sgrR" 1 1 1 "sgrR"
"sroA" 1 1 1 "sroA"
"tbpA" 1 1 1 "thiB"
"thiP" 1 1 1 "thiP"
"thiQ" 1 1 1 "thiQ"
"sgrT" 1 1 1 1 "sgrT"
"sgrS" 1 1 1 1 "sgrS"
"setA" 1 1 1 1 "setA"
"leuL" 1 1 "leuL"
"leuA" 1 1 "leuA"
"leuB" 1 1 "leuB"
"leuC" 1 1 "leuC"
"leuD" 1 1 "leuD"
"leuO" 1 1 "leuO"
"ilvI" -1 "ilvI"
"ilvH" -1 "ilvH"
"ftsQ" 1 1 1 "ftsQ"
"ftsA" 1 1 1 "ftsA"
"ftsZ" 1 1 1 "ftsZ"
"pcnB" -1 -1 1 1 "pcnB"
"folK" -1 -1 1 1 "folK"
"dksA" -1 -1 -1 1 "dksA"
"gluQ" -1 -1 -1 1 "gluQ"
"tff" -1 1 "tff"
"rpsB" -1 1 "rpsB"
"tsf" -1 1 "tsf"
"frr" -1 1 "frr"
"rrsH" -1 -1 -1 1 1 "rrsH"
"ileV" -1 -1 -1 1 1 "ileV"
"alaV" -1 -1 -1 1 1 "alaV"
"rrlH" -1 -1 -1 1 1 "rrlH"
"rrfH" -1 -1 -1 1 1 "rrfH"
"yahO" 1 "yahO"
"iraP" 1 1 1 "iraP"
"yaiA" 1 "yaiA"
"aroM" 1 "aroM"
"queA" -1 "queA"
"tgt" -1 "tgt"
"yajC" -1 "yajC"
"yajO" 1 "yajO"
"bolA" 1 1 1 "bolA"
"ybaA" 1 "ybaA"
"ybaS" 1 1 "glsA"
"ybaT" 1 1 "ybaT"
"ybdK" 1 "ybdK"
"ybeL" 1 "ybeL"
"metT" -1 1 "metT"
"leuW" -1 1 "leuW"
"glnU" -1 1 "glnU"
"glnW" -1 1 "glnW"
"metU" -1 1 "metU"
"glnV" -1 1 "glnV"
"glnX" -1 1 "glnX"
"ybgA" 1 1 "ybgA"
"phr" 1 1 "phr"
"ybgS" 1 "ybgS"
"ybhP" 1 "ybhP"
"clsB" 1 "clsB"
"ybhN" 1 "ybhN"
"dps" 1 1 1 "dps"
"dacC" 1 1 "dacC"
"ybjP" 1 1 "ybjP"
"poxB" 1 1 1 "poxB"
"cspD" 1 1 "cspD"
"infA" -1 "infA"
"serW" -1 1 "serW"
"lrp" 1 1 "lrp"
"ftsK" 1 1 "ftsK"
"ycaP" 1 "ycaP"
"rmf" 1 "rmf"
"yccT" 1 "yccT"
"yccU" 1 "yccU"
"cbpA" 1 1 "cbpA"
"cbpM" 1 1 "cbpM"
"agp" 1 "agp"
"wrbA" 1 1 "wrbA"
"yccJ" 1 1 "yccJ"
"csgD" 1 1 1 "csgD"
"csgE" 1 1 1 "csgE"
"csgF" 1 1 1 "csgF"
"csgG" 1 1 1 "csgG"
"msyB" 1 1 "msyB"
"grxB" 1 1 "grxB"
"rluC" -1 "rluC"
"ariR" 1 "ariR"
"ycgB" 1 "ycgB"
"treA" 1 1 "treA"
"pth" -1 1 "pth"
"ychF" -1 1 "ychF"
"ychH" 1 1 "ychH"
"tyrT" -1 1 "tyrT"
"tyrV" -1 1 "tyrV"
"tpr" -1 1 "tpr"
"rssB" 1 1 "rssB"
"acnA" 1 1 "acnA"
"osmB" 1 1 "osmB"
"uspE" 1 "uspE"
"ydcK" 1 "ydcK"
"ydcL" 1 "ydcL"
"curA" 1 "curA"
"narU" 1 1 "narU"
"adhP" 1 "adhP"
"sra" 1 1 "sra"
"osmC" 1 1 "osmC"
"gadB" 1 1 1 "gadB"
"gadC" 1 1 1 "gadC"
"tam" 1 1 "tam"
"ynfD" 1 "ynfD"
"sodC" 1 1 "sodC"
"cfa" 1 1 1 "cfa"
"ynhG" 1 "ldtE"
"sufA" 1 1 "sufA"
"sufB" 1 1 "sufB"
"sufC" 1 1 "sufC"
"sufD" 1 1 "sufD"
"sufS" 1 1 "sufS"
"sufE" 1 1 "sufE"
"yniA" 1 "yniA"
"katE" 1 1 "katE"
"yeaG" 1 1 "yeaG"
"yeaH" 1 1 "yeaH"
"yeaQ" 1 "yeaQ"
"fadD" 1 1 "fadD"
"sroD" 1 1 "sroD"
"yoaC" 1 1 "yoaC"
"yebV" 1 "yebV"
"yebF" 1 "yebF"
"argS" -1 1 "argS"
"uspC" 1 "uspC"
"otsB" 1 1 "otsB"
"otsA" 1 1 "otsA"
"yedP" 1 "yedP"
"hchA" 1 1 "hchA"
"fbaB" 1 1 "fbaB"
"yehE" 1 "yehE"
"osmF" 1 1 "osmF"
"yehY" 1 1 "yehY"
"yehX" 1 1 "yehX"
"yehW" 1 1 "yehW"
"yohC" 1 "yohC"
"yojI" 1 1 "yojI"
"elaB" 1 1 "elaB"
"argT" -1 1 "argT"
"hisJ" -1 1 "hisJ"
"hisQ" -1 1 "hisQ"
"hisM" -1 1 "hisM"
"hisP" -1 1 "hisP"
"yfcZ" 1 "yfcZ"
"fadL" 1 1 "fadL"
"talA" 1 1 1 "talA"
"tktB" 1 1 1 "tktB"
"hmp" 1 1 1 "hmp"
"rpoE" 1 1 1 1 1 "rpoE"
"rseA" 1 1 1 1 1 "rseA"
"rseB" 1 1 1 1 1 "rseB"
"rseC" 1 1 1 1 1 "rseC"
"rrsG" -1 -1 -1 1 1 "rrsG"
"gltW" -1 -1 -1 1 1 "gltW"
"rrlG" -1 -1 -1 1 1 "rrlG"
"rrfG" -1 -1 -1 1 1 "rrfG"
"csiD" 1 1 "glaH"
"lhgO" 1 1 "lhgD"
"gabD" 1 1 1 "gabD"
"gabT" 1 1 1 "gabT"
"gabP" 1 1 1 "gabP"
"ygaU" 1 1 "kbp"
"yqaE" 1 "yqaE"
"csrA" 1 1 1 1 "csrA"
"rpoS" -1 1 "rpoS"
"mazE" -1 "mazE"
"mazF" -1 "mazF"
"mazG" -1 "mazG"
"relA" 1 1 "relA"
"mazE" 1 1 "mazE"
"mazF" 1 1 "mazF"
"csrB" 1 1 1 1 "csrB"
"metZ" -1 1 "metZ"
"metW" -1 1 "metW"
"metV" -1 1 "metV"
"prfB" -1 "prfB"
"lysS" -1 "lysS"
"speC" -1 1 "speC"
"yghA" 1 "yghA"
"dkgA" 1 1 "dkgA"
"glgS" 1 1 "glgS"
"patA" 1 1 1 "patA"
"yqjF" 1 "yqjF"
"yhbO" 1 "yhbO"
"rpsO" -1 "rpsO"
"pnp" -1 "pnp"
"yhcO" 1 "yhcO"
"dusB" -1 -1 1 "dusB"
"fis" -1 -1 1 "fis"
"rrsD" -1 -1 -1 1 1 "rrsD"
"ileU" -1 -1 -1 1 1 "ileU"
"alaU" -1 -1 -1 1 1 "alaU"
"rrlD" -1 -1 -1 1 1 "rrlD"
"rrfD" -1 -1 -1 1 1 "rrfD"
"thrV" -1 -1 -1 1 1 "thrV"
"rrfF" -1 -1 -1 1 1 "rrfF"
"fkpA" 1 1 "fkpA"
"crp" -1 "crp"
"glgC" 1 1 "glgC"
"glgA" 1 1 "glgA"
"glgP" 1 1 "glgP"
"ggt" 1 "ggt"
"yhhA" 1 "yhhA"
"livJ" 1 1 1 "livJ"
"uspB" 1 1 "uspB"
"uspA" 1 1 "uspA"
"dtpB" 1 "dtpB"
"hdeA" 1 1 1 "hdeA"
"hdeB" 1 1 1 "hdeB"
"yhiD" 1 1 1 "yhiD"
"hdeD" 1 1 1 "hdeD"
"gadE" 1 1 "gadE"
"gadF" 1 1 "gadF"
"mdtE" 1 1 "mdtE"
"mdtF" 1 1 "mdtF"
"gadX" 1 1 1 "gadX"
"gadA" 1 1 1 "gadA"
"treF" 1 1 "treF"
"yjaG" 1 1 "yjaG"
"cspA" -1 1 "cspA"
"ivbL" 1 1 "ivbL"
"ilvB" 1 1 "ilvB"
"ilvN" 1 1 "ilvN"
"dnaA" -1 1 "dnaA"
"dnaN" -1 1 "dnaN"
"recF" -1 1 "recF"
"rpmH" -1 "rpmH"
"rnpA" -1 "rnpA"
"mnmG" -1 1 1 "mnmG"
"rsmG" -1 1 1 "rsmG"
"mioC" -1 "mioC"
"rrsC" -1 -1 -1 1 1 "rrsC"
"gltU" -1 -1 -1 1 1 "gltU"
"rrlC" -1 -1 -1 1 1 "rrlC"
"rrfC" -1 -1 -1 1 1 "rrfC"
"ilvL" 1 1 "ilvL"
"ilvX" 1 1 "ilvX"
"ilvG_1" 1 1 "ilvG"
"ilvM" 1 1 "ilvM"
"ilvE" 1 1 "ilvE"
"ilvD" 1 1 "ilvD"
"ilvA" 1 1 "ilvA"
"trxA" 1 1 "trxA"
"argX" -1 -1 1 1 "argX"
"hisR" -1 -1 1 1 "hisR"
"leuT" -1 -1 1 1 "leuT"
"proM" -1 -1 1 1 "proM"
"ysgA" 1 1 "ysgA"
"rrsA" -1 -1 -1 1 1 "rrsA"
"ileT" -1 -1 -1 1 1 "ileT"
"alaT" -1 -1 -1 1 1 "alaT"
"rrlA" -1 -1 -1 1 1 "rrlA"
"rrfA" -1 -1 -1 1 1 "rrfA"
"csrC" 1 1 1 "csrC"
"yiiS" 1 1 "yiiS"
"uspD" 1 1 "uspD"
"rpmE" -1 1 "rpmE"
"argH" 1 "argH"
"rrsB" -1 -1 -1 1 1 "rrsB"
"gltT" -1 -1 -1 1 1 "gltT"
"rrlB" -1 -1 -1 1 1 "rrlB"
"rrfB" -1 -1 -1 1 1 "rrfB"
"thrU" -1 1 "thrU"
"tyrU" -1 1 "tyrU"
"glyT" -1 1 "glyT"
"thrT" -1 1 "thrT"
"tufB" -1 1 "tufB"
"rrsE" -1 -1 -1 1 1 "rrsE"
"gltV" -1 -1 -1 1 1 "gltV"
"rrlE" -1 -1 -1 1 1 "rrlE"
"rrfE" -1 -1 -1 1 1 "rrfE"
"yjbJ" 1 "yjbJ"
"qor" 1 "qorA"
"cadA" -1 "cadA"
"efp" -1 1 "efp"
"ecnB" 1 1 "ecnB"
"blc" 1 1 "blc"
"aidB" 1 1 1 "aidB"
"yjfY" 1 "yjfY"
"rpsF" -1 1 "rpsF"
"priB" -1 1 "priB"
"rpsR" -1 1 "rpsR"
"rplI" -1 1 "rplI"
"cysQ" 1 "cysQ"
"pyrL" -1 "pyrL"
"pyrB" -1 "pyrB"
"pyrI" -1 "pyrI"
"yjgH" 1 "yjgH"
"argI" 1 1 1 "argI"
"leuX" -1 1 "leuX"
"fimB" 1 1 1 "fimB"
"ytiC" 1 -1 1 "ytiC"
"ytiD" 1 -1 1 "ytiD"
"idlP" 1 -1 1 1 "idlP"
"iraD" 1 -1 1 1 "iraD"
"leuV" -1 "leuV"
"prfC" -1 "prfC"
"osmY" 1 1 1 "osmY"
"thrL" 1 1 "thrL"
"rpsT" -1 "rpsT"
"rybB" 1 1 1 "rybB"
"rpsA" -1 1 "rpsA"
"ihfB" -1 1 "ihfB"
"fabH" -1 "fabH"
"fabD" -1 "fabD"
"fabG" -1 "fabG"
"fadR" -1 1 "fadR"
"thrS" -1 "thrS"
"infC" -1 1 "infC"
"rpmI" -1 1 "rpmI"
"rplT" -1 1 "rplT"
"pheM" -1 "pheM"
"pheS" -1 "pheS"
"pheT" -1 "pheT"
"ihfA" -1 "ihfA"
"dsrA" 1 1 "dsrA"
"hisL" 1 "hisL"
"hisG" 1 "hisG"
"hisD" 1 "hisD"
"hisC" 1 "hisC"
"hisB" 1 "hisB"
"hisH" 1 "hisH"
"hisA" 1 "hisA"
"hisF" 1 "hisF"
"hisI" 1 "hisI"
"rplY" -1 1 "rplY"
"rpsP" -1 1 "rpsP"
"rimM" -1 1 "rimM"
"trmD" -1 1 "trmD"
"rplS" -1 1 "rplS"
"rpoS" 1 "rpoS"
"rpsU" -1 1 "rpsU"
"dnaG" -1 1 "dnaG"
"rpoD" -1 1 "rpoD"
"rplU" -1 1 "rplU"
"rpmA" -1 1 "rpmA"
"yhbE" -1 1 "yhbE"
"obgE" -1 1 "obgE"
"rplM" -1 1 "rplM"
"rpsI" -1 1 "rpsI"
"rpsM" -1 1 "rpsM"
"rpsK" -1 1 "rpsK"
"rpsD" -1 1 "rpsD"
"rpoA" -1 1 "rpoA"
"rplQ" -1 1 "rplQ"
"rplN" -1 "rplN"
"rplX" -1 "rplX"
"rplE" -1 "rplE"
"rpsN" -1 "rpsN"
"rpsH" -1 "rpsH"
"rplF" -1 "rplF"
"rplR" -1 "rplR"
"rpsE" -1 "rpsE"
"rpmD" -1 "rpmD"
"rplO" -1 "rplO"
"secY" -1 "secY"
"rpmJ" -1 "rpmJ"
"rpsJ" -1 1 "rpsJ"
"rplC" -1 1 "rplC"
"rplD" -1 1 "rplD"
"rplW" -1 1 "rplW"
"rplB" -1 1 "rplB"
"rpsS" -1 1 "rpsS"
"rplV" -1 1 "rplV"
"rpsC" -1 1 "rpsC"
"rplP" -1 1 "rplP"
"rpmC" -1 1 "rpmC"
"rpsQ" -1 1 "rpsQ"
"rpsL" -1 "rpsL"
"rpsG" -1 "rpsG"
"fusA" -1 "fusA"
"tufA" -1 "tufA"
"rpmB" -1 "rpmB"
"rpmG" -1 "rpmG"
"mutM" -1 "mutM"
"rpoZ" -1 1 "rpoZ"
"spoT" -1 1 "spoT"
"trmH" -1 1 "trmH"
"recG" -1 1 "recG"
"rplK" -1 "rplK"
"rplA" -1 "rplA"
"rplJ" -1 "rplJ"
"rplL" -1 "rplL"
"rpoB" -1 "rpoB"
"rpoC" -1 "rpoC"