{"text_format":"2","workbook":"xls","n_sheets":7,"sheets":["most regulating TFs","EC","BS","PA","MT","CG","SA"],"not_rendered":{"charts":0,"images":0,"macros":0,"external_links":0,"defined_names":0,"comments":0,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1900","formulas":"cached_only"}

{"sheet":"most regulating TFs","index":0,"n_rows":122,"n_cols":6,"rows_kept":122,"cut":false,"hidden":false,"merged":[],"flags":["formulas_cached_only"]}
["Table 1. Most regulating and regulated transcription factors. The transcription and sigma factors with the most highest output/inputs degrees are show for each bacterium regulatory network."]
[]
["Organism","Regulator","Type","Dominance level","# Inputs","# Outputs"]
["E. coli"]
[null,"CRP","TF",2,2,428]
[null,"FNR","TF",1,2,277]
[null,"FIS","TF",1,3,218]
[null,"IHF","TF",4,3,214]
[null,"ArcA","TF",2,2,157]
[null,"H-NS","TF",1,4,136]
[null,"NarL","TF",2,3,113]
[null,"Lrp","TF",2,3,95]
[null,"NsrR","TF",1,0,83]
[null,"Fur","TF",1,4,83]
[null,"GadX","TF",1,11,24]
[null,"FlhDC","TF",6,10,79]
[null,"RpoH","SF",5,8,6]
[null,"GadE","TF",1,6,30]
[null,"MarA","TF",1,6,30]
[null,"MarR","TF",5,6,2]
[null,"CsgD","TF",8,6,12]
[null,"GadW","TF",2,5,13]
[null,"CaiF","TF",3,5,10]
[null,"RpoS","SF",3,5,9]
["B. subtilis"]
[null,"SigA","SF",1,3,740]
[null,"CcpA","TF",1,0,189]
[null,"Comk","TF",1,6,181]
[null,"SigE","SF",5,5,179]
[null,"Abrb","TF",1,2,150]
[null,"SigB","SF",2,1,103]
[null,"SigG","SF",1,5,97]
[null,"SigW","SF",2,1,94]
[null,"SigD","SF",2,1,81]
[null,"SpoIIID","TF",6,1,70]
[null,"Comk","TF",1,6,181]
[null,"SigG","SF",1,5,97]
[null,"SpoIIAB","AS",5,5,0]
[null,"PhoP","TF",6,5,39]
[null,"HutP","TF",3,4,4]
[null,"SigF","SF",4,4,45]
[null,"SinR","TF",4,4,22]
[null,"HrcA","TF",4,4,10]
["P. aeruginosa"]
[null,"LasR","TF",2,6,95]
[null,"RpoN","SF",1,0,73]
[null,"Fur","TF",6,1,68]
[null,"MexT","TF",4,1,47]
[null,"PvdS","ECF",8,3,46]
[null,"ArgR","TF",1,0,44]
[null,"Anr","TF",1,1,44]
[null,"AlgU","ECF",1,5,40]
[null,"PmrA","TF",3,1,33]
[null,"Dnr","TF",4,2,33]
[null,"LasR","TF",2,6,95]
[null,"RhlR","TF",3,6,27]
[null,"AlgU","ECF",1,5,40]
[null,"ExsA","TF",1,4,18]
[null,"PtxR","TF",1,4,12]
[null,"RpoS","SF",4,4,13]
[null,"FleQ","TF",5,4,23]
[null,"PtxS","TF",2,3,5]
[null,"PvdS","ECF",8,3,46]
["M. tuberculosis"]
[null,"Rv0348","TF",2,1,296]
[null,"Rv1221","SF",1,3,282]
[null,"Rv0757","TF",1,0,247]
[null,"Rv3676","TF",1,0,235]
[null,"Rv0491","TF",1,0,222]
[null,"Rv0981","TF",2,1,210]
[null,"Rv3286c","SF",1,1,151]
[null,"Rv2711","TF",1,4,144]
[null,"Rv2710","TF",4,4,143]
[null,"Rv3291c","TF",2,1,92]
[null,"Rv3133c","TF",3,8,59]
[null,"Rv0353","TF",4,8,8]
[null,"Rv2711","TF",1,4,144]
[null,"Rv2710","TF",4,4,143]
[null,"Rv0967","TF",3,4,3]
[null,"Rv1343c","TF",3,4,1]
[null,"Rv1221","SF",1,3,282]
[null,"Rv1909c","TF",4,3,5]
[null,"Rv1846c","TF",5,3,25]
["C. glutamicum"]
[null,"GlxR","TF",1,1,150]
[null,"DtxR","TF",1,0,64]
[null,"RamB","TF",3,3,52]
[null,"LexA","TF",2,2,48]
[null,"McbR","TF",1,1,46]
[null,"SugR","TF",1,1,39]
[null,"AmtR","TF",1,0,37]
[null,"PhoR","TF",1,1,18]
[null,"CysR","TF",2,1,18]
[null,"RamA","TF",2,2,18]
[null,"AcnR","TF",4,5,2]
[null,"Frur","TF",2,4,5]
[null,"RamB","TF",3,3,52]
[null,"VanR","TF",1,2,3]
[null,"ArgR","TF",2,2,8]
[null,"cg3082","TF",2,2,4]
[null,"GspR","TF",3,2,7]
[null,"ClgR","TF",4,2,8]
[null,"PyrR","TF",4,2,4]
["S. aureus"]
[null,"CodY","TF",1,0,146]
[null,"CcpA","TF",1,0,121]
[null,"Fur","TF",3,1,47]
[null,"Rex","TF",1,0,38]
[null,"SaeR","TF",1,0,30]
[null,"CymR","TF",1,0,21]
[null,"ArgR","TF",1,0,15]
[null,"LexA","TF",1,0,15]
[null,"PerR","TF",2,1,15]
[null,"PurR","TF",1,0,14]
[null,"ArcR","TF",2,3,3]
[]
[]
[]
[null,"AS= Anti-sigma factor"]
[null,"SF= Sigma factor"]
[null,"TF= Transcriptional factor"]
[null,"ECF= Extracitoplasmatic factor"]

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["Table 2A. Biological function of transcription factors and sigma factors of transcription regulatory network of E. coli.  "]
[]
["Transcription factor","Type","Dominance level","Biological function ",{"$nulls":4},"in degree","out degree"]
["AcrR","TF",1,"repressor local of stress signal",{"$nulls":4},0,3]
["Ada","TF",4,"Adaptive response to alkylating agents",{"$nulls":4},2,3]
["AdiY","TF",1,"N-acetylgalactosamine metabolism",{"$nulls":4},0,1]
["AgaR","TF",2,"Assimilation of allantoin nitrogen",{"$nulls":4},1,8]
["AlaS","TF",1,"AlpA DNA-binding transcriptional activator; CP4-57 prophage",{"$nulls":4},0,0]
["AllR","TF",1,"Allantoin utilization",{"$nulls":4},0,10]
["AllS","TF",2,"Allose transcriptional activator",{"$nulls":4},1,3]
["AlpA","TF",1,"AlpA DNA-binding transcriptional activator; CP4-57 prophage",{"$nulls":4},0,1]
["AppY","TF",2,"Induced by starvation for Pi and by entry into stationary phase",{"$nulls":4},1,10]
["AraC","TF",3,"Arabinose metabolism",{"$nulls":4},2,10]
["ArcA","TF",2,"Aerobic regulatory protein",{"$nulls":4},2,157]
["ArgP","TF",3," Initiator for oriC replication",{"$nulls":4},1,7]
["ArgR","TF",2,"Arginine biosynthesis",{"$nulls":4},1,36]
["ArsR","TF",1," arsenic detoxification",{"$nulls":4},0,2]
["AscG","TF",2,"Criptic regulator for the transport of arbutin, salicin, and cellobiose",{"$nulls":4},1,4]
["AsnC","TF",7,"Asparagine synthetase A transcription",{"$nulls":4},2,3]
["AtoC","TF",1,"AtoC transcriptional activator; Az protein inhibitor of ODC",{"$nulls":4},0,4]
["BaeR","TF",3,"Indole induces the expression of multidrug exporter",{"$nulls":4},1,8]
["BetI","TF",3,"Choline and osmotic stress",{"$nulls":4},2,3]
["BglJ","TF",3,"Transport and utilization of the aromatic beta-glucosides arbutin and salicin",{"$nulls":4},2,3]
["BirA","TF",1,"Biotin biosynthesis",{"$nulls":4},0,5]
["BolA","TF",6,"Cell morphology ",{"$nulls":4},4,2]
["CadC","TF",6,"Operon as a function of pH and lysine",{"$nulls":4},4,2]
["CaiF","TF",3,"Carnitine metabolism",{"$nulls":4},5,10]
["Cbl","TF",6,"Organic sulphur assimilation",{"$nulls":4},3,9]
["CdaR","TF",1,"regulator of enzymes involved in D-galactarate, D-glucarate, and D-glycerate utilization",{"$nulls":4},0,9]
["ChbR","TF",4,"Utilization of cellobiose, chitobiose",{"$nulls":4},2,5]
["CpxR","TF",2,"Envelope stress response",{"$nulls":4},1,55]
["CreB","TF",1,"Carbon catabolism",{"$nulls":4},0,1]
["Crp","TF",2,"Catabolic regulatory protein",{"$nulls":4},2,428]
["CsgD","TF",8,"Master regulator for biofilm formation-gene regulation",{"$nulls":4},6,12]
["CsiR","TF",1,"Carbon starvation induced Regulator, DNA-binding transcriptional repressor",{"$nulls":4},0,5]
["CspA","TF",9,"Control and regulation of the cellular responses to cold shock",{"$nulls":4},4,2]
["CspB","TF",1,"Control and regulation of the cellular responses to cold shock",{"$nulls":4},0,1]
["CspC","TF",1,"Control and regulation of the cellular responses to cold shock",{"$nulls":4},0,1]
["CueR","TF",1,"Copper homeostasis",{"$nulls":4},0,7]
["CusR","TF",2,"Copper-responsive two-component system",{"$nulls":4},1,5]
["CynR","TF",2,"Use of cyanate as a sole nitrogen source",{"$nulls":4},1,3]
["CysB","TF",2,"Sulfonate-sulfur metabolism",{"$nulls":4},1,23]
["CytR","TF",3,"Regulation of cytidine metabolism",{"$nulls":4},2,11]
["DcuR","TF",3,"C4-dicarboxylates",{"$nulls":4},4,7]
["DeoR","TF",1,"Deoxyribonucleoside utilization",{"$nulls":4},0,6]
["DgsA","TF",6,"Negative regulator of the mannose PTS",{"$nulls":4},3,9]
["DhaR","TF",1,"dihydroxyacetone kinase controls DNA-binding transcriptional dual regulator",{"$nulls":4},0,3]
["DicA","TF",1,"Division cell regulator",{"$nulls":4},0,2]
["DnaA","TF",4,"Regulator of DNA replication",{"$nulls":4},1,10]
["DsdC","TF",2,"D-serine deaminase synthesis",{"$nulls":4},2,2]
["EnvR","TF",1,"EnvR DNA-binding transcriptional repressor",{"$nulls":4},0,2]
["EnvY","TF",1,"EnvY DNA-binding transcriptional activator",{"$nulls":4},0,2]
["EvgA","TF",2,"Regulation of drug efflux genes",{"$nulls":4},1,13]
["ExuR","TF",1,"Regulation of hexuronate system",{"$nulls":4},0,7]
["FabR","TF",1,"Fatty acid biosynthesis",{"$nulls":4},0,2]
["FadR","TF",1,"fatty acid biosynthetic gene",{"$nulls":4},0,11]
["FeaR","TF",3,"2-phenylethylamine catabolism",{"$nulls":4},2,1]
["FecI","SF",1,"Sigma for ferric citrate transport system.",{"$nulls":4},2,1]
["FecR","TF",9,"Ferric citrate transport system.",{"$nulls":4},3,1]
["FhlA","TF",5,"Formate hydrogen lyase regulation",{"$nulls":4},4,29]
["Fis","TF",1,"Nucleid-associated protein, exponential phase",{"$nulls":4},3,218]
["FlhDC","TF",6,"master regulator for flagellar and motility systems",{"$nulls":4},10,79]
["FliA","SF",7,"Flagellar sigma factor",{"$nulls":4},4,0]
["Fnr","TF",1,"Fumarate-nitrate regulatory protein (anaerobic)",{"$nulls":4},2,277]
["FruR","TF",1,"catabolite repressor-activator protein",{"$nulls":4},0,40]
["FucR","TF",3,"L-fucose pathway",{"$nulls":4},2,6]
["Fur","TF",1,"Global regulator of iron uptake systems",{"$nulls":4},4,83]
["GadE","TF",1,"Activator involved in the response to acid ",{"$nulls":4},6,30]
["GadW","TF",2,"Glutamate-dependent acid resistance",{"$nulls":4},5,13]
["GadX","TF",1,"Glutamate-dependent acid resistance",{"$nulls":4},11,24]
["GalR","TF",1,"Galactose regulon",{"$nulls":4},2,9]
["GalS","TF",3,"Galactose regulon",{"$nulls":4},3,9]
["GatR_1","TF",1,"negative DNA-binding transcriptional regulator of galactitol metabolism",{"$nulls":4},0,6]
["GatR_2","TF",1,"GatR, split galactitol utilization operon repressor, fragment 2",{"$nulls":4},0,6]
["GcvA","TF",2,"Glycine cleavage operon",{"$nulls":4},1,4]
["GlcC","TF",3,"Activated by growth on glycolate",{"$nulls":4},3,6]
["GlnG","TF",5,"Glutamine/glutamate levels",{"$nulls":4},4,43]
["GlpR","TF",3,"Glycerol utilization",{"$nulls":4},1,9]
["GlrR","TF",1,"GlrR DNA-binding transcriptional activator TC",{"$nulls":4},0,1]
["GntR","TF",2,"Gluconate catabolism",{"$nulls":4},1,12]
["GutM","TF",1,"Mediate metabolism of glucitol (i.e., sorbitol)",{"$nulls":4},4,6]
["HcaR","TF",1,"regulation of genes involved in the oxidative stress response.",{"$nulls":4},0,5]
["HdfR","TF",2,"Regulator for the flagellar master operon",{"$nulls":4},1,1]
["HipA","TF",1,"serine/threonine kinase HipA",{"$nulls":4},2,1]
["HipB","TF",5,"Affects lethality due to inhibition of peptidoglycan or DNA synthesis",{"$nulls":4},3,1]
["Hns","TF",1,"Nucleid-associated protein, mid-log phase",{"$nulls":4},4,136]
["Hu","TF",3,"Nucleid-associated protein",{"$nulls":4},2,9]
["HyfR","TF",6,"Induced under fermentative conditions by formate at a low pH",{"$nulls":4},4,11]
["IclR","TF",2,"Glyoxylate bypass",{"$nulls":4},1,3]
["IdnR","TF",3,"L-idonate catabolism",{"$nulls":4},2,6]
["Ihf","TF",4,"Nucleoid-associated protein, stationary phase",{"$nulls":4},3,214]
["IlvY","TF",2,"Isoleucine-valine biosynthetic pathway",{"$nulls":4},1,1]
["IscR","TF",2,"Activator in response to oxidative stress",{"$nulls":4},1,25]
["KdgR","TF",1,"Pectin and polygalacturonate ",{"$nulls":4},0,1]
["KdpE","TF",1,"KdpE transcriptional activator",{"$nulls":4},0,4]
["LacI","TF",1,"Lactose utilization",{"$nulls":4},0,3]
["LeuO","TF",2,"LeuO DNA-binding transcriptional dual activator",{"$nulls":4},1,11]
["LexA","TF",2,"SOS regulation",{"$nulls":4},1,54]
["LldR","TF",4,"L-lactate metabolism",{"$nulls":4},2,2]
["LrhA","TF",1,"regulator of flagella, motility and chemotaxis",{"$nulls":4},0,2]
["Lrp","TF",2,"Leucine-responsive regulatory protein",{"$nulls":4},3,95]
["LsrR","TF",3,"Quorum sensing; Biofilm formation",{"$nulls":4},1,8]
["LysR","TF",2,"Regulation of leucine, alanine metabolism",{"$nulls":4},1,1]
["MalI","TF",3,"Regulation of the maltose system",{"$nulls":4},2,2]
["MalT","TF",7,"Maltodextrin system",{"$nulls":4},4,10]
["MarA","TF",1,"Multidrug resistance regulator",{"$nulls":4},6,30]
["MarR","TF",5,"Multidrug resistance regulator",{"$nulls":4},6,2]
["MelR","TF",3,"Melibiose operon",{"$nulls":4},2,2]
["MetJ","TF",2,"Methionine metabolism",{"$nulls":4},2,15]
["MetR","TF",3,"Methionine metabolism",{"$nulls":4},1,5]
["MhpR","TF",1,"MhpR transcriptional activator, propionic acid",{"$nulls":4},0,6]
["MngR","TF",2,"Regulation of the transport of the osmolyte 2-O-alpha-mannosyl-D-glycerate",{"$nulls":4},1,2]
["MntR","TF",1,"Manganese homeostasis",{"$nulls":4},0,1]
["ModE","TF",1,"molybdate-dependent transcriptional regulator",{"$nulls":4},0,46]
["MprA","TF",2,"Reduces the synthesis of peptide microcins B17 and C7",{"$nulls":4},1,4]
["MqsA","TF",1,"MqsR and MqsA (YgiT) are a toxin/antitoxin (TA) pair",{"$nulls":4},1,1]
["MqsR","TF",2,"MqsR and MqsA (YgiT) are a toxin/antitoxin (TA) pair",{"$nulls":4},1,1]
["MtlR","TF",3,"Mannitol repressor",{"$nulls":4},4,2]
["MurR","TF",1,"N-acetylmuramate utilization",{"$nulls":4},0,2]
["Nac","TF",6,"Nitrogen assimilation control",{"$nulls":4},2,14]
["NadR","TF",1,"NAD biosynthesis",{"$nulls":4},0,4]
["NagC","TF",3,"Amino sugar biosynthesis and degradation",{"$nulls":4},2,19]
["NanR","TF",1,"N-acetylneuraminic acid",{"$nulls":4},0,8]
["NarL","TF",2,"Nitrate-responsive regulator",{"$nulls":4},3,113]
["NarP","TF",1,"Nitrate and nitrite respiration",{"$nulls":4},0,49]
["NemR","TF",2,"N-ethylmaleimide reductase repressor",{"$nulls":4},1,1]
["NhaR","TF",2,"Cation-responsive protein",{"$nulls":4},1,6]
["NikR","TF",3,"Nickel-specific response",{"$nulls":4},2,5]
["NorR","TF",2,"Senses nitric oxide",{"$nulls":4},1,2]
["NrdR","TF",1,"Ribonucleotide reductases",{"$nulls":4},0,8]
["NsrR","TF",1,"Nitrosative stress response",{"$nulls":4},0,83]
["OmpR","TF",5,"Porins regulation for envelope stress response",{"$nulls":4},3,15]
["OxyR","TF",4,"Antioxidant response",{"$nulls":4},3,21]
["PaaX","TF",1,"Phenylacetic acid degradation",{"$nulls":4},0,12]
["PdhR","TF",3,"Pyruvate dehydrogenase complex regulator",{"$nulls":4},3,19]
["PepA","TF",1,"aminopeptidase A/I",{"$nulls":4},0,2]
["PhoB","TF",2,"Phosphorus assimilation",{"$nulls":4},1,36]
["PhoP","TF",6,"Sensing external magnesium availability",{"$nulls":4},1,34]
["PrpR","TF",3,"Propionate catabolic pathways",{"$nulls":4},3,4]
["PspF","TF",2,"Phague shock regulator",{"$nulls":4},1,6]
["PurR","TF",2,"Purine and pyrimidine",{"$nulls":4},2,30]
["PutA","TF",2,"Oxidation of L-proline to glutamate",{"$nulls":4},2,1]
["QseB","TF",2,"Autoinducer 2 controls motility",{"$nulls":4},1,2]
["RbsR","TF",3,"D-ribose metabolism",{"$nulls":4},2,5]
["RcnR","TF",2,"Nickel, cobalt and iron homeostasis",{"$nulls":4},1,1]
["RcsAB","TF",2,"Acetyl phosphate-sensitive regulation",{"$nulls":4},3,21]
["RelEB","TF",1,"Qin prophage; toxin of the RelE-RelB toxin-antitoxin system and cofactor to enhance the repressor activity of RelB",{"$nulls":4},0,1]
["RhaR","TF",3,"Regulate expression of the l-rhamnose catabolic regulon in response to l-rhamnose availability",{"$nulls":4},3,1]
["RhaS","TF",1,"Regulate expression of the l-rhamnose catabolic regulon in response to l-rhamnose availability",{"$nulls":4},3,5]
["Rob","TF",2,"Multidrug resistance regulator",{"$nulls":4},1,18]
["RpiR","TF",1,"Allose use regulator, DNA-binding transcriptional repressor",{"$nulls":4},0,5]
["RpoD","SF",1,"House-keeping sigma",{"$nulls":4},3,80]
["RpoE","SF",3,"Sigma for maintaining the integrity of periplasmic and outer membrane components",{"$nulls":4},1,3]
["RpoH","SF",5,"Heat-shock sigma",{"$nulls":4},8,6]
["RpoN","SF",4,"Nitrogen transcription sigma",{"$nulls":4},2,6]
["RpoS","SF",3,"Stres generalized sigma",{"$nulls":4},5,9]
["RstA","TF",7,"Drug resistance",{"$nulls":4},1,10]
["RtcR","TF",1,"RNA terminal phosphate cyclase regulator",{"$nulls":4},0,2]
["RutR","TF",1,"pyrimidine sensor",{"$nulls":4},0,15]
["SdiA","TF",1,"SdiA DNA-binding transcriptional dual regulator",{"$nulls":4},0,4]
["SgrR","TF",1,"SugaR transport-related Regulator",{"$nulls":4},0,6]
["SlyA","TF",1,"Activates expression of genes such as molecular chaperones ",{"$nulls":4},0,1]
["SoxR","TF",2,"Oxidative stress response",{"$nulls":4},1,2]
["SoxS","TF",4,"Oxidative stress response",{"$nulls":4},3,33]
["SrlR","TF",3,"Mediate metabolism of glucitol (i.e., sorbitol)",{"$nulls":4},4,6]
["StpA","TF",3,"H-NS-like DNA-binding protein with RNA chaperone activity",{"$nulls":4},2,3]
["TdcA","TF",5,"Transport and metabolism of threonine and serine during anaerobic growth",{"$nulls":4},4,6]
["TdcR","TF",1,"transport and metabolism of threonine and serine during anaerobic growth",{"$nulls":4},0,7]
["TorR","TF",1,"respiratory system upon trimethylamine N-oxide electron-acceptor",{"$nulls":4},0,11]
["TreR","TF",7,"Trehalose system",{"$nulls":4},3,2]
["TrpR","TF",2,"Tryptophan operon regulation",{"$nulls":4},1,11]
["TyrR","TF",2,"Aromatic amino acid biosynthesis and transport",{"$nulls":4},1,11]
["UhpA","TF",1,"UhpA transcriptional activator TC",{"$nulls":4},0,1]
["UidR","TF",1,"β-d-glucuronides repressor, DNA-binding transcriptional repressor",{"$nulls":4},0,3]
["UlaR","TF",1,"Ascorbate utilization",{"$nulls":4},0,7]
["UxuR","TF",3,"Regulation of hexuronate system",{"$nulls":4},2,6]
["XapR","TF",1,"Xanthosine utilization",{"$nulls":4},0,2]
["XylR","TF",3,"D-xylose operons",{"$nulls":4},3,5]
["YdeO","TF",6,"Glutamate-dependent acid resistance",{"$nulls":4},2,3]
["YefM","TF",1,"YefM antitoxin of the YoeB-YefM toxin-antitoxin pair and DNA binding transcriptional repressor",{"$nulls":4},1,1]
["YeiL","TF",5,"Might function as a post-exponential-phase nitrogen-starvation regulator?",{"$nulls":4},4,0]
["YiaJ","TF",5,"Unknown carbohydrate which generates the intermediate L-xylulose",{"$nulls":4},3,9]
["YoeB","TF",2,"Toxin of the YoeB-YefM toxin-antitoxin pair",{"$nulls":4},1,1]
["ZntR","TF",1,"Zinc resistance",{"$nulls":4},0,1]
["ZraR","TF",5,"Zinc, lead efflux pumps?",{"$nulls":4},2,2]
["Zur","TF",1,"Zinc homeostasis",{"$nulls":4},0,6]

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["Table 2B. Biological function of transcription factors and sigma factors of transcription regulatory network of B. subtilis.  "]
[]
["Transcription factor","Type","Dominance level","Biological function ",{"$nulls":4},"in degree","out degree"]
["AbrB","TF",1,"Regulation of transition state genes (essential for competence)",{"$nulls":4},2,150]
["AcoR","TF",2,"Positive regulation of the acetoin dehydrogenase operon",{"$nulls":4},2,4]
["AdaA","TF",2,"Adaptative response to DNA alkylation",{"$nulls":4},1,2]
["AhrC","TF",1,"Negative regulation of arginine biosynthesis and positive regulation of arginine catabolism ",{"$nulls":4},0,13]
["AlsR","TF",1,"Regulation of the alpha-acetolactate operon ",{"$nulls":4},0,3]
["AnsR","TF",1,"Repressor of the ans operon coding for L-asparaginase and L-aspartase",{"$nulls":4},0,2]
["AraR","TF",2,"Negative regulation of the L-arabinose metabolic operon",{"$nulls":4},1,8]
["ArfM","TF",3,"Activation of anaerobic respiratory and fermentative loci (nasDE, hmp, lctE, alsSD)",{"$nulls":4},2,19]
["ArsR","TF",2,"Arsenic resistance operon repressor",{"$nulls":4},1,3]
["AzlB","TF",1,"Conferring resistance to a leucine analog, 4-azaleucine ",{"$nulls":4},0,1]
["BirA","TF",1,"negative regulation of the biotin operon",{"$nulls":4},0,7]
["BkdR","TF",1,"Involved in the control of isoleucine and valine utilization as sole nitrogen sources",{"$nulls":4},0,7]
["BltR","TF",1,"Regulation of the bltD operon, multidrug response",{"$nulls":4},0,1]
["BmrR","TF",3,"Positive regulation of the bmrUR operon",{"$nulls":4},3,1]
["CcpA","TF",1,"Carbon catabolite control protein involved in glucose regulation of several genes",{"$nulls":4},0,189]
["CcpB","TF",2,"Mediates catabolite repression by glucose, mannitol, and sucrose of gluconate (gnt) and xylose (xyl) operons",{"$nulls":4},1,6]
["CcpC","TF",2,"Carbon catabolite and anaerobic repression of citB and citZ",{"$nulls":4},2,8]
["CggR","TF",2,"Repression of gapA expression, Its inducer is Fru1,6P",{"$nulls":4},1,5]
["CitR","TF",2,"Negative regulation of the citrate synthase I gene (citA)",{"$nulls":4},1,1]
["CitT","TF",1,"Involved in the response to the environmental Mg-citrate complex",{"$nulls":4},0,1]
["CodY","TF",2,"DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase and sporulation.",{"$nulls":4},1,56]
["ComA","TF",2,"Positive regulation of late competence genes and surfactin production ",{"$nulls":4},1,15]
["ComK","TF",1,"Final autoregulatory control switch prior to competence development",{"$nulls":4},6,181]
["CssR","TF",2,"Involved in the control of cellular responses to protein secretion stress",{"$nulls":4},1,3]
["CtsR","TF",3,"Negative regulation of class III stress genes (clpC, clpP, clpE)",{"$nulls":4},2,11]
["DctR","TF",2,"Involved in C4-dicarboxylate transport",{"$nulls":4},2,1]
["DegU","TF",2,"Essential for degradative enzyme (sacB and degQ) expression and competence regulation (positive regulation of comK expression)",{"$nulls":4},1,18]
["DeoR","TF",2,"Negative regulation of the dra-nupC-pdp operon (deoxyribonucleoside)",{"$nulls":4},2,3]
["DnaA","TF",2,"Initiation of chromosome replication",{"$nulls":4},1,2]
["ExuR","TF",6,"Repression of the hexuronate utilization operon (uxaC-yjmBCD-uxuA-yjmf-exuTR-uxaBA)",{"$nulls":4},3,8]
["Fnr","TF",2,"Anaerobic regulator",{"$nulls":4},2,7]
["FruR","TF",1,"Negative regulation of the fructose operon (fruRBA)",{"$nulls":4},0,1]
["Fur","TF",3,"Negative regulation of siderophore biosynthesis and transcription of ferri-siderophore uptake genes",{"$nulls":4},2,50]
["GabR","TF",2,"Positive regulation of gabTD and negative autoregulation, presence and absence of GABA",{"$nulls":4},1,2]
["GerE","TF",7,"Required for the expression of late spore coat genes",{"$nulls":4},1,42]
["GlcT","TF",1,"Antitermination protein regulates the expression of the ptsG gene",{"$nulls":4},0,3]
["GlnR","TF",3,"Negative regulation of the glutamine synthetase gene (glnA)",{"$nulls":4},2,9]
["GlpP","TF",1,"Control of mRNA stability of glpD",{"$nulls":4},0,5]
["GltC","TF",2,"Positive regulation of the glutamate synthase operon (gltAB)",{"$nulls":4},1,2]
["GltR","TF",2,"Negative regulation of the glutamate synthase operon (gltAB)",{"$nulls":4},1,2]
["GntR","TF",3,"Negative regulation of the gluconate operon (gntRKPZ)",{"$nulls":4},3,3]
["GutB","TF",3,"Sorbitol dehydrogenase",{"$nulls":4},2,0]
["GutR","TF",2,"Sorbitol utilization",{"$nulls":4},1,1]
["Hpr","TF",3,"Negative regulation of sporulation and extracellular proteases genes (aprE, nprE, sin)",{"$nulls":4},2,10]
["HrcA","TF",4,"Negative regulation of class I heat-shock genes (dnaK, groESL)",{"$nulls":4},4,10]
["HutP","TF",3,"Positive regulation of the histidine utilization operon (hutPHUIGM)",{"$nulls":4},4,4]
["HxlR","TF",1,"Activator of the hxlAB operon involved in the detoxification of formaldehyde",{"$nulls":4},0,2]
["IolR","TF",2,"Negative regulation of the myo-inositol catabolism operon (iolABCDEFGHIJ/iolRS)",{"$nulls":4},1,10]
["KdgR","TF",2,"Negative regulation of the pectin utilization operon (kdgRKAT)",{"$nulls":4},2,3]
["KipR","TF",3,"Regulator of the kip operon for gamma-Hexachlorocyclohexane degradation",{"$nulls":4},1,5]
["LacR","TF",1,"Negative regulation of the beta-galactosidase gene (lacA)",{"$nulls":4},0,2]
["LevR","TF",1,"Positive regulation of the levanase operon (levDEFG/sacC)",{"$nulls":4},0,1]
["LexA","TF",2,"SOS regulation",{"$nulls":4},1,54]
["LicR","TF",2,"Positive regulation of the lichenan operon (licBCAH)",{"$nulls":4},1,1]
["LicT","TF",3,"Required for substrate-dependent induction and catabolite repression of bglPH",{"$nulls":4},3,4]
["LmrA","TF",2,"Negative regulation of the lincomycin operon (lmrBA)",{"$nulls":4},1,2]
["LrpA","TF",1,"Negative regulation of glyA transcription, serine hydroxymethyltransferase, and KinB-dependent sporulation",{"$nulls":4},0,1]
["LrpB","TF",1,"Negative regulation of glyA transcription, serine hydroxymethyltransferase and KinB-dependent sporulation",{"$nulls":4},0,1]
["LrpC","TF",2,"Transcriptional regulator (Lrp/AsnC family)",{"$nulls":4},1,0]
["LytR","TF",3,"Attenuator role for lytABC and lytR expression",{"$nulls":4},3,3]
["Med","TF",2,"Positive regulator of comK",{"$nulls":4},1,1]
["MntR","TF",1,"Regulation of manganese transport (repression of mntH in high Mn(II) conditions, activation of mntABCD under low Mn(II) conditions)",{"$nulls":4},0,3]
["Mta","TF",2,"Positive regulation of multidrug-efflux transporter genes (bmr and blt)",{"$nulls":4},1,4]
["MtrB","TF",2,"Regulation of tryptophan biosynthesis (required for transcription (and translation) attenuation in the trp operon); repression of the folate operon",{"$nulls":4},1,21]
["PaiA","TF",1,"Negative regulation of sporulation, septation and degradative enzyme genes (aprE, nprE, phoA, sacB)",{"$nulls":4},0,1]
["PaiB","TF",1,"Negative regulation of sporulation and degradative enzyme genes",{"$nulls":4},0,1]
["PerR","TF",2,"Negative regulation of the peroxide regulon (mrgA, katA, ahpCF)",{"$nulls":4},1,51]
["PhoP","TF",6,"Involved in phosphate regulation (phoA, phoB, phoD, resABCDE, tagAB, tagDEF, tuaA-H)",{"$nulls":4},5,39]
["PucR","TF",3,"Regulation of puc genes, purine catabolism",{"$nulls":4},2,14]
["PurR","TF",1,"negative regulation of the purine operons (purEKBCLQFMNHD, purA)",{"$nulls":4},0,32]
["PyrR","TF",2,"Attenuation (antitermination) of the pyrimidine operon (pyrPBCADFE) in the presence of UMP",{"$nulls":4},2,9]
["ResD","TF",1,"Activation role in global regulation of aerobic and anaerobic respiration (resA, ctaA, qcrABC, fnr, lctEP)",{"$nulls":4},2,53]
["RocR","TF",2,"Positive regulation of arginine utilization operons (rocABC, rocDEF, rocG)",{"$nulls":4},1,7]
["Rok","TF",5,"Repressor of comK",{"$nulls":4},3,27]
["RsbW","AS",3,"Anti-sigma sigB",{"$nulls":4},2,0]
["RsiX","AS",3,"Anti-sigma sigX",{"$nulls":4},3,0]
["SacT","TF",2,"Antiterminator of sacA and sacP, b-glucosides",{"$nulls":4},1,7]
["SacY","TF",3,"Positive regulation of levansucrase and sucrase synthesis",{"$nulls":4},3,6]
["SenS","TF",2,"Positive regulation of extracellular enzyme genes (amyE, aprE, nprE)",{"$nulls":4},1,1]
["SigA","SF",1,"House-keeping sigma",{"$nulls":4},3,740]
["SigB","SF",2,"General stress response",{"$nulls":4},1,103]
["SigD","SF",2,"Chemotaxis/autolysin/flagellar gene expression",{"$nulls":4},1,81]
["SigE","SF",5,"Early mother cell gene expression (sporulation)",{"$nulls":4},5,179]
["SigF","SF",4,"Early forespore gene expression (sporulation)",{"$nulls":4},4,45]
["SigG","SF",1,"Late forespore gene expression (sporulation)",{"$nulls":4},5,97]
["SigH","SF",2,"Postexponential gene expression; competence and early sporulation genes",{"$nulls":4},3,48]
["SigI","SF",2,"The sigI gene is heat shock induced",{"$nulls":4},1,1]
["SigL","SF",2,"Degradative enzyme gene expression",{"$nulls":4},1,19]
["SigM","ECF",2,"Activated in Response to Cell Wall Antibiotics, Ethanol, Heat, Acid, and Superoxide Stress",{"$nulls":4},1,9]
["SigW","ECF",2,"Controls genes involved in transport processes and detoxification.",{"$nulls":4},1,94]
["SigX","ECF",2,"SigX may be involved in the regulation of iron metabolism",{"$nulls":4},2,29]
["SigY","ECF",1,"Putative ECF, cell envelope stress",{"$nulls":4},0,5]
["SinR","TF",4,"Regulation of post-exponential-phase responses genes (positive regulation of comK; negative regulation of aprE, kinB, sigD, spo0A, spoIIA, spoIIE, spoIIG)",{"$nulls":4},4,22]
["Spo0A","TF",3,"Central role in the initiation of sporulation (negative regulation of abrB, kinA, kinC, spo0A; positive regulation of spoIIA, spoIIE, spoIIG)",{"$nulls":4},2,37]
["SpoIIAB","AS",5,"Anti-sigma sigF",{"$nulls":4},5,0]
["SpoIIID","TF",6,"SpoIIID is a key regulator of transcription in the mother cell and positively or negatively regulates more than 100 genes",{"$nulls":4},1,70]
["SpoIVCB","SF",8,"Late mother cell gene expression (sporulation)",{"$nulls":4},3,0]
["SpoVT","TF",2,"Positive and negative regulation of sigma-G-dependent genes",{"$nulls":4},1,38]
["TenA","TF",2,"Positive regulation of extracellular enzyme genes (aprE, nprE, phoA, sacB)",{"$nulls":4},1,5]
["TenI","TF",1,"Positive regulation of extracellular proteases",{"$nulls":4},0,6]
["TnrA","TF",2,"Global nitrogen regulation (positive regulation of nrgAB, nasBCDEF, gabP, ureABC, guaD; negative regulation of glnRA, gltAB)",{"$nulls":4},2,60]
["TreR","TF",2,"Negative regulation of the trehalose operon (trePAR)",{"$nulls":4},2,1]
["Xpf","TF",1,"Required for expression of the PBSX late operon, control of bacterial suicide",{"$nulls":4},0,10]
["Xre","TF",1,"PBSX is a phage-like bacteriocin (phibacin), repressor",{"$nulls":4},0,4]
["XylR","TF",1,"Negative regulation of the xylose operon (xylAB)",{"$nulls":4},0,3]
["YbbM","AS",3,"Anti-sigma sigW",{"$nulls":4},2,0]
["YcbA","TF",1,"Two-component system positively regulates the expression of the glsA-glnT (formerly ybgJ-ybgH) operon",{"$nulls":4},0,1]
["YdiH","TF",1,"YdiH Is a Direct Negative Regulator of acetate production",{"$nulls":4},0,5]
["YfhP","TF",2,"Unknown; similar to unknown protein",{"$nulls":4},1,3]
["YflA","TF",4,"Unknown; similar to aminoacid carrier protein (ohrR)",{"$nulls":4},1,0]
["YhdL","AS",3,"Anti-sigma sigM",{"$nulls":4},2,0]
["YkmA","TF",1,"Organic hydroperoxide resistance transcriptional regulator",{"$nulls":4},0,1]
["YlaC","ECF",2,"This sigma factor contributes to oxidative stress resistance",{"$nulls":4},1,0]
["YlbO","TF",6,"Regulates the expression of some coat proteins during sporulation in B. subtilis directly or indirectly.",{"$nulls":4},1,17]
["YocG","TF",1,"Regulation of cold shock expression of (desR)",{"$nulls":4},0,1]
["YrhI","TF",3,"yrhI (renamed bscR) encodes a repressor that negatively regulates the transcription of the bscR-CYP102A3 cytochrome P450 .",{"$nulls":4},2,1]
["YrxA","TF",2,"YrxA is the regulator of NAD de novo biosynthesis",{"$nulls":4},1,4]
["YrzC","TF",2,"Master regulator of sulfur metabolism",{"$nulls":4},1,21]
["YtlI","TF",3,"Unknown; similar to transcriptional regulator (LysR family)",{"$nulls":4},2,7]
["YtrA","TF",2,"Ytr transport system plays a role in acetoin utilization during stationary phase and sporulation.",{"$nulls":4},1,3]
["YufM","TF",1,"Similar to two-component response regulator",{"$nulls":4},0,2]
["YvbA","TF",2,"Represses the transcription of the sdpIR operon and of several other operons that probably contribute to delaying commitment to sporulation",{"$nulls":4},3,5]
["YvrH","TF",1,"Two-component regulatory system YvrG/YvrH ",{"$nulls":4},0,13]
["YvrI","ECF",2,"Essential for Acid Stress Induction of Oxalate Decarboxylase",{"$nulls":4},1,0]
["YwfK","TF",2,"CysL (formerly YwfK), a LysR-type transcriptional regulator, activates the transcription of the cysJI operon, which encodes sulfite reductase.",{"$nulls":4},1,2]
["YxlC","AS",2,"Anti-sigma sigY",{"$nulls":4},1,0]
["YycF","TF",1,"Member of the two-component regulatory system yycG/yycF ",{"$nulls":4},0,7]
["Zur","TF",1,"Zinc-specific repression of operons implicated in zinc uptake (yciC, ycdHI-yceA)",{"$nulls":4},0,5]

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["Table 2C. Biological function of transcription factors and sigma factors of transcription regulatory network of P. aeruginosa.  "]
[]
["Transcription factor","Type","Dominance level","Biological function ",{"$nulls":4},"in degree","out degree"]
["AgmR","TF",9,"Identified to be involved in the regulation of the quinoprotein ethanol oxidation system",{"$nulls":4},1,11]
["AguR","TF",1,"Possible interactions between AguR and the regulatory region of the aguBA operon utilizes agmatine as the sole carbon and nitrogen source)",{"$nulls":4},0,2]
["AlgQ","TF",1,"AlgQ is a global regulatory protein which activates alginate and AlgqQ is Involvement   in Transcriptional Regulation of Pyoverdine Genes",{"$nulls":4},0,3]
["AlgR","TF",3,"AlgR controls a variety of virulence factors, including alginate production, twitching motility, biofilm formation, quorum sensing, and hydrogen cyanide (HCN) production.",{"$nulls":4},2,30]
["AlgR3","TF",1,"Involved in alginate synthesis",{"$nulls":4},0,1]
["AlgR4","TF",1,"Involved in alginate synthesis",{"$nulls":4},0,1]
["AlgU","ECF",1,"Alginate biosynthesis",{"$nulls":4},5,40]
["AlgW","TF",1,"PPS: controlling protease activity, alginate biosynthesis",{"$nulls":4},0,2]
["AlgZ","TF",4,"DB: two-component signal transduction system (phosphorelay).                                         Pps: alginate production",{"$nulls":4},2,13]
["AmpR","TF",1,"Resistance a  -lactam antibiotics and aminoglycosides",{"$nulls":4},0,7]
["Anr","TF",1,"Anaerobic regulator, ANR acts as an oxygen sensor, regulating gene expression according to oxygen availability",{"$nulls":4},1,44]
["ArgR","TF",1,"ArgR makes physical contact with ANR and thereby facilitates initiation of arc transcription",{"$nulls":4},0,44]
["BexR","TF",1,"Epigenetic Control of Virulence Gene Expression",{"$nulls":4},0,6]
["BqsR","TF",1,"BqsS-BqsR that regulates biofilm decay in P. aeruginosa.",{"$nulls":4},0,4]
["BqsS","TF",1,"BqsS-BqsR that regulates biofilm decay in P. aeruginosa.",{"$nulls":4},0,4]
["CbrB","TF",1,"The CbrA-CbrB two-component regulatory system controls the utilization of multiple carbon and nitrogen sources in Pseudomonas aeruginosa.",{"$nulls":4},0,13]
["CysB","TF",1,"CysB can act as an activator of algD expression, alginate",{"$nulls":4},0,19]
["Dnr","TF",4,"Response to oxygen tension and NO.",{"$nulls":4},2,33]
["ExsA","TF",1,"Type III secretion system (T3SS",{"$nulls":4},4,18]
["ExsD","TF",2,"Type III secretion system (T3SS",{"$nulls":4},1,1]
["FhpR","TF",2,"Stress by paraquat, hydrogen peroxide, and tert-butyl hydroperoxide",{"$nulls":4},2,1]
["FleQ","TF",5,"Regulates mucin adhesion and motility (flagellar genes expression)",{"$nulls":4},4,23]
["FlgM","AS",2,"Role in motility",{"$nulls":4},1,2]
["FliA","SF",1,"Flagellar sigma factor",{"$nulls":4},1,4]
["FoxI","ECF",7,"These data suggested that these epithelial cells served as an iron source",{"$nulls":4},1,0]
["FpvI","ECF",8,"Regulation of pyoverdine production and uptake",{"$nulls":4},1,1]
["FpvR","AS",7,"Regulation of pyoverdine production and uptake",{"$nulls":4},1,2]
["Fur","TF",6,"Regulator of iron uptake ",{"$nulls":4},1,68]
["GacA","TF",1,"Activation of multiple extracellular virulence factors as well as chronic persistence genes, including those required for biofilm formation and N-acyl-homoserine lactone  autoinducers (Reimmann et al., 1997; Parkins et al., 2001). GacS mutants are also impaired in swarming motility",{"$nulls":4},0,6]
["GacS","TF",1,"GacS/GacA, regulates a variety of virulence and stress-responsive genes, and is involved in the formation of biofilms.",{"$nulls":4},0,2]
["GbuR","TF",7,"The arginine dehydrogenase (ADH; also called arginine oxidase)\npathway",{"$nulls":4},1,2]
["GlpR","TF",8,"Regulator of the glycerol uptake system, glycerol kinase and\nG3P dehydrogenase",{"$nulls":4},1,6]
["GpuR","TF",1,"Responsible for 3-guanidinopropionate utilization, as thecarbon and nitrogen source",{"$nulls":4},0,2]
["HasR","ECF",7,"Captures free or haemoglobin-bound haem and shuttles it to a specic cell surface outer membrane receptor",{"$nulls":4},1,0]
["Hu","TF",1,"Exotoxin A production ",{"$nulls":4},0,1]
["Ihf","TF",1,"Control alginate biosynthesis by algD regulation",{"$nulls":4},0,30]
["LasR","TF",2,"Control the Quorum sensing",{"$nulls":4},6,95]
["MetR","TF",1,"Swarming motility controlled",{"$nulls":4},0,9]
["MexR","TF",3,"Negatively regulates multidrug\nefflux systems. resistance to a variety of antimicrobial agents.",{"$nulls":4},1,5]
["MexT","TF",4,"Antibiotic resistance",{"$nulls":4},1,47]
["MexZ","TF",2,"Antibiotic resistance",{"$nulls":4},1,2]
["MucA","AS",2,"Anti-sigma of algU, alginate biosynthesis",{"$nulls":4},1,1]
["MucB","TF",2,"Alginate bisynthesis, mucoid phenotype",{"$nulls":4},1,1]
["MucC","TF",1,"Alginate bisynthesis, mucoid phenotype",{"$nulls":4},0,1]
["MucD","TF",1,"Alginate bisynthesis, mucoid phenotype",{"$nulls":4},0,1]
["MvaT","TF",1,"MvaTrepresses the transcription of cup genes for fimbria",{"$nulls":4},0,3]
["MvfR","TF",4,"MvfR is required to produce virulence factors, such as pyocyanin and hydrogen cyanide, and a large family of 4-hydroxy-2-alkylquinolines (HAQs), including the intercellular signals 3,4-dihydroxy-2-heptylquinoline (PQS) and 4-hydroxy-2-heptylquinoline (HHQ)  which function in the transcriptional regulation of multiple virulence genes",{"$nulls":4},2,8]
["MvtA","TF",1,"Alginate bisynthesis, mucoid phenotype",{"$nulls":4},0,1]
["NalC","TF",4,"Antibiotic resistance",{"$nulls":4},1,3]
["NarL","TF",5,"Anaerobic Regulatory",{"$nulls":4},2,12]
["NfxB","TF",1,"Involved in conferring resistance to quinolones",{"$nulls":4},0,0]
["OspR","TF",1,"Constitutive expression of ospR alters pigment production and b-lactam resistance in P. aeruginosa",{"$nulls":4},0,1]
["PA0779","TF",1,"Responds to reactive nitrogen species and is also capable of protecting cells against nitrosative stress and reactive oxygen species",{"$nulls":4},0,2]
["PA1300","ECF",7,"Iron uptake regulator proteins",{"$nulls":4},1,0]
["PA1301","AS",7,"Iron uptake regulator proteins",{"$nulls":4},1,0]
["PA3409","AS",7,"Iron uptake regulator proteins",{"$nulls":4},1,0]
["PA3697","TF",1,"Implicated in the protection from reactive oxygen species",{"$nulls":4},0,1]
["PA3899","ECF",7,"Iron uptake regulator proteins",{"$nulls":4},1,0]
["PA3900","AS",7,"Iron uptake regulator proteins",{"$nulls":4},1,0]
["PA4895","AS",7,"Iron uptake regulator proteins",{"$nulls":4},1,0]
["PA4896","ECF",7,"Iron uptake regulator proteins",{"$nulls":4},1,0]
["PA5471","TF",1,"Resistance to, antibiotics",{"$nulls":4},0,1]
["PchR","TF",7,"Production of exotoxin A (ETA) and the pyoverdine and pyochelin  siderophores",{"$nulls":4},1,7]
["PfeR","TF",7,"Required for the enterobactin-inducible production of the ferric enterobactin receptor (PfeA)",{"$nulls":4},1,1]
["PhhR","TF",1,"Regulator of the cluster of structural genes encoding phenylalanine hydroxylase (PhhA), carbinolamine dehydratase (PhhB), and aromatic aminotransferase (PhhC)",{"$nulls":4},0,3]
["PhoP","TF",1,"Resistant to cationic antimicrobial peptides and polymyxin B.",{"$nulls":4},0,18]
["PhoQ","TF",2,"Resistant to cationic antimicrobial peptides and polymyxin B.",{"$nulls":4},1,3]
["PilA","TF",2,"PilA, Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]",{"$nulls":4},2,0]
["PilR","TF",1,"Pilin biosynthesis",{"$nulls":4},0,2]
["PmrA","TF",3,"Resistant to cationic antimicrobial peptides and polymyxin B.",{"$nulls":4},1,33]
["PprB","TF",1,"Antibiotic resistance and susceptibility",{"$nulls":4},2,2]
["PpyR","TF",1,"Increases biofilm formation in Pseudomonas aeruginosa PAO1",{"$nulls":4},0,1]
["PqrR","TF",1,"Paraquat response",{"$nulls":4},0,3]
["PsdR","TF",1," Pseudomonas dipeptide regulator",{"$nulls":4},0,5]
["PsrA","TF",1,"Responds to long-chain fatty acid signals to regulate the fadBA5 beta-oxidation operon",{"$nulls":4},0,13]
["PtxR","TF",1,"Modulate the expression of toxA, the exotoxin A-encoding gene",{"$nulls":4},4,12]
["PtxS","TF",2,"Production of exotoxin A",{"$nulls":4},3,5]
["PvdS","ECF",8,"The regulation of pyoverdine production and uptake ",{"$nulls":4},3,46]
["QscR","TF",1,"Quorum sensing repressor",{"$nulls":4},0,1]
["RcsB","TF",1,"Two component regulator of the operon cup",{"$nulls":4},0,5]
["RhlR","TF",3,"Virulence, bacterial conjugation, bioluminescence and biofilm formation",{"$nulls":4},6,27]
["RocA1","TF",1,"Transcriptional regulator",{"$nulls":4},0,2]
["RocR","TF",1,"Transcriptional regulator",{"$nulls":4},0,2]
["RoxR","TF",1,"RoxSR in the expression of the terminal oxidase genes, plays an important role in the regulation of respiration in P. aeruginosa.",{"$nulls":4},0,17]
["RoxS","TF",1,"RoxSR in the expression of the terminal oxidase genes,  plays an important role in the regulation of respiration in P. aeruginosa.",{"$nulls":4},0,17]
["RpoD","SF",2,"House-keeping sigma",{"$nulls":4},1,3]
["RpoH","SF",2,"Heat-shock sigma",{"$nulls":4},1,0]
["RpoN","SF",1,"Play important roles in motility, in the transport of nutrients, in the formation of pili, in mucoidy and in cell-to-cell signalling",{"$nulls":4},0,73]
["RpoS","SF",4,"The secretion of extracellular virulence factors",{"$nulls":4},4,13]
["RsaL","TF",3,"Virulence genes, and genes involved in biofilm formation and antibiotic resistance",{"$nulls":4},2,1]
["ToxR","TF",9,"Production of exotoxin A (ETA) ",{"$nulls":4},1,8]
["TpbA","TF",3,"Represses biofilm formation ",{"$nulls":4},2,12]
["TrpI","TF",1,"Activates the expression of the trpBA genes encoding the two tryptophan synthase subunits",{"$nulls":4},0,2]
["Vfr","TF",1,"Controls global virulence factor expression through cyclic AMP-dependent and -independent",{"$nulls":4},0,7]
["VqsM","TF",1,"AraC-type transcriptional regulator\nVqsM is a novel QS modulator, which positively controls production of N-acylhomoserine lactones (AHLs) and virulence factors in P. aeruginosa",{"$nulls":4},0,3]
["VqsR","TF",2,"VqsR is involved in the regulation of the expression of certain sets of virulence and quorum- sensing controlled genes ",{"$nulls":4},2,1]
["VreI","ECF",1,"Regulator virulence",{"$nulls":4},0,3]

{"sheet":"MT","index":4,"n_rows":86,"n_cols":10,"rows_kept":86,"cut":false,"hidden":false,"merged":[[2,3,2,7]],"flags":["formulas_cached_only"]}
["Table 2D. Biological function of transcription factors and sigma factors of transcription regulatory network of M. tuberculosis.  "]
[]
["Transcription factor","Type","Dominance level","Biological function ",{"$nulls":4},"in degree","out degree"]
["Rv0001","TF",2,"Plays an important role in the initiation and regulation of chromosomal replication. Binds to the origin of replication",{"$nulls":4},2,4]
["Rv0117","TF",3,"OxyS, oxidative stress response protein regulatory protein, LysR family ",{"$nulls":4},1,22]
["Rv0144","TF",7,"Transcriptional regulator, tetR-family",{"$nulls":4},2,0]
["Rv0182c","SF",2,"Sigma factor SigG",{"$nulls":4},1,83]
["Rv0212c","TF",3,"Response to host immune response ",{"$nulls":4},2,5]
["Rv0260c","TF",1,"Possible transcriptional regulatory protein",{"$nulls":4},0,7]
["Rv0302","TF",1,"Probable transcription regulatory protein, TetR family ",{"$nulls":4},0,4]
["Rv0348","TF",2,"Transcriptional regulator",{"$nulls":4},1,296]
["Rv0353","TF",4,"Involved in transcriptional regulation (repression) of heat shock protein",{"$nulls":4},8,8]
["Rv0445c","SF",1,"Alternative RNA polymerase sigma factor SigK",{"$nulls":4},0,33]
["Rv0465c","TF",3,"Uncharacterized HTH-type transcriptional regulator Rv0465c/MT0481",{"$nulls":4},1,4]
["Rv0485","TF",2,"Transcriptional regulator",{"$nulls":4},2,24]
["Rv0491","TF",1,"Sensory transduction protein regX3",{"$nulls":4},0,222]
["Rv0494","TF",1,"Transcriptional regulator, gntR-family",{"$nulls":4},0,14]
["Rv0576","TF",1,"Transcriptional regulator, arsR-family",{"$nulls":4},0,1]
["Rv0586","TF",2,"Transcriptional regulator, gntR-family",{"$nulls":4},1,18]
["Rv0735","SF",1,"Probable alternative RNA polymerase sigma factor SigL",{"$nulls":4},0,5]
["Rv0757","TF",1,"Two component regulatory system PHOP/PHOQ. This protein is thought to be a positive regulator for the phosphate regulon, required for intracellular growth",{"$nulls":4},0,247]
["Rv0818","TF",1,"Two-component system, OmpR family, response regulator",{"$nulls":4},0,14]
["Rv0823c","TF",3,"tRNA-dihydrouridine synthase",{"$nulls":4},1,4]
["Rv0844c","TF",1,"Possible nitrate/nitrite response transcriptional regulatory protein NarL",{"$nulls":4},0,9]
["Rv0967","TF",3,"Involved in transcriptional mechanism; repression of the CSO operon.",{"$nulls":4},4,3]
["Rv0981","TF",2,"Regulator part of a two component regulatory system (MPRAB system",{"$nulls":4},1,210]
["Rv1027c","TF",1,"Member of the two-component regulatory system KDPD/KDPE involved in the regulation of the KDP operon.",{"$nulls":4},0,3]
["Rv1033c","TF",1,"Sensor part of the two component regulatory system TRCS/TRCR. ",{"$nulls":4},0,1]
["Rv1221","SF",1,"Alternative RNA polymerase sigma factor SigE",{"$nulls":4},3,282]
["Rv1266c","TF",1,"Involved in signal transduction (via phosphorylation). Thought to be involved in arabinan metabolism, ",{"$nulls":4},0,1]
["Rv1267c","TF",2,"Thought to regulate the biosynthesis of the mycobacterial cell wall arabinan and resistance to ethambutol",{"$nulls":4},2,3]
["Rv1316c","TF",1,"Repair of alkylated guanine in DNA by stoichiometrically transferring the alkyl group at the O-6 position to a cysteine residue in the enzyme.",{"$nulls":4},0,4]
["Rv1343c","TF",3,"Probable conserved lipoprotein LprD",{"$nulls":4},4,1]
["Rv1359","TF",1,"Transcriptional regulator",{"$nulls":4},0,23]
["Rv1379","TF",4,"Binds to the conserved sequence in the PYR operon mRNA and disrupts the antiterminator, permitting terminator hairpin formation and promoting transcription termination",{"$nulls":4},1,6]
["Rv1395","TF",1,"Transcriptional regulator cytochrome P450",{"$nulls":4},0,31]
["Rv1404","TF",2," Transcriptional regulatory protein",{"$nulls":4},1,1]
["Rv1657","TF",2,"Probable arginine repressor ArgR (",{"$nulls":4},1,14]
["Rv1675c","TF",1," Probable cmr, cAMP and macrophage regulator, transcriptional regulatory protein",{"$nulls":4},0,7]
["Rv1785c","TF",1,"Cytochrome P450 143 cyp143",{"$nulls":4},0,12]
["Rv1846c","TF",5,"Transcriptional regulator BlaI",{"$nulls":4},3,25]
["Rv1909c","TF",4,"Acts as a global negative controlling element, employing FE(2+) as a cofactor to bind the operator of the repressed genes.",{"$nulls":4},3,5]
["Rv1931c","TF",1,"Transcriptional regulator",{"$nulls":4},2,19]
["Rv1956","TF",3,"Antitoxin, transcriptional regulator",{"$nulls":4},1,25]
["Rv1963c","TF",1,"TetR-family transcriptional repressor mce3R",{"$nulls":4},0,33]
["Rv1985c","TF",1,"ArgP family transcriptional regulator",{"$nulls":4},0,3]
["Rv1990c","TF",2,"Transcriptional regulator",{"$nulls":4},2,1]
["Rv1994c","TF",1,"Metal sensor transcriptional regulator CmtR (ArsR-SmtB family)",{"$nulls":4},0,2]
["Rv2017","TF",1,"Transcriptional regulator",{"$nulls":4},0,8]
["Rv2021c","TF",1,"Transcriptional regulator",{"$nulls":4},0,9]
["Rv2034","TF",2,"ArsR-type repressor protein",{"$nulls":4},1,23]
["Rv2069","SF",6,"RNA polymerase sigma factor, ECF subfamily, SigC",{"$nulls":4},2,44]
["Rv2175c","TF",1,"Uncharacterized protein",{"$nulls":4},0,4]
["Rv2358","TF",2,"ArsR family transcriptional regulator",{"$nulls":4},2,1]
["Rv2359","TF",1,"Acts as a global negative controlling element, employing Zn(2+) as a cofactor to bind the operator of the repressed genes.",{"$nulls":4},2,56]
["Rv2374c","TF",1,"Probable heat shock protein transcriptional repressor HrcA",{"$nulls":4},0,8]
["Rv2669","TF",2,"Probable acetyltransferase",{"$nulls":4},2,3]
["Rv2710","TF",4,"May control the regulons of stationary phase and general stress resistance",{"$nulls":4},4,143]
["Rv2711","TF",1,"Transcriptional regulatory protein (repressor and activator), iron-binding repressor of siderophore biosynthesis and iron uptake",{"$nulls":4},4,144]
["Rv2720","TF",3,"Involved in regulation of nucleotide excision repair and sos response. Represses a number of genes involved in the response to DNA damage (sos response), including RECA and LEXA",{"$nulls":4},1,40]
["Rv2745c","TF",2,"Transcriptional regulator",{"$nulls":4},2,12]
["Rv3080c","TF",3," Involved in transcriptional regulatory mechanism and in the regulation of secondary metabolites [catalytic activity: ATP + a protein = ADP + a phosphoprotein].",{"$nulls":4},2,8]
["Rv3082c","TF",1,"May have a role in the regulation of proteins necessary for virulence.",{"$nulls":4},0,7]
["Rv3133c","TF",3,"Transcriptional regulatory protein devR (DosR)",{"$nulls":4},8,59]
["Rv3164c","TF",2,"Involved in transcriptional mechanism; regulates methanol dehydrogenase.",{"$nulls":4},1,1]
["Rv3223c","SF",3,"SigH Alternative sigma factor that plays a role in the oxidative-stress response (regulation of thioredoxin recycling)",{"$nulls":4},1,50]
["Rv3279c","TF",1,"BIRA acts both as a biotin-operon repressor and as the enzyme that synthesizes the corepressor, acetyl-CoA:carbon-dioxide ligase. ",{"$nulls":4},0,4]
["Rv3286c","SF",1,"sigF Thought to be involved in survival and proliferation in lung granulomas during infection. Thought to be involved in virulence and persistence processes. ",{"$nulls":4},1,151]
["Rv3291c","TF",2,"Probable transcriptional regulatory protein LrpA (Lrp/AsnC-family)",{"$nulls":4},1,92]
["Rv3328c","SF",1,"Probable alternative RNA polymerase sigma factor (fragment) SigJ",{"$nulls":4},0,1]
["Rv3334","TF",1,"Transcriptional regulator, merR-family",{"$nulls":4},0,7]
["Rv3414c","SF",3,"Probable alternative RNA polymerase sigma-D factor SigD",{"$nulls":4},1,16]
["Rv3416","TF",1,"Involved in transcriptional mechanism (growth phase-dependent).",{"$nulls":4},0,50]
["Rv3557c","TF",1,"HTH-type transcriptional repressor KstR2",{"$nulls":4},0,8]
["Rv3574","TF",1,"Involved in transcriptional mechanism. Predicted to control regulon involved in lipid metabolism",{"$nulls":4},0,80]
["Rv3575c","TF",1,"Uncharacterized protein",{"$nulls":4},0,24]
["Rv3648c","TF",2,"Probable cold shock protein A CspA",{"$nulls":4},1,3]
["Rv3676","TF",1,"Transcriptional regulatory protein Crp (Crp/Fnr-family)",{"$nulls":4},0,235]
["Rv3678c","TF",1,"Uncharacterized protein",{"$nulls":4},0,8]
["Rv3681c","TF",1,"Transcriptional regulator WhiB4",{"$nulls":4},0,8]
["Rv3692","TF",1,"Involved in transcriptional mechanism; regulates methanol dehydrogenase",{"$nulls":4},0,14]
["Rv3744","TF",1,"Metal sensor transcriptional regulator (ArsR-SmtB family)",{"$nulls":4},0,1]
["Rv3833","TF",1,"Transcriptional regulator, araC-family",{"$nulls":4},0,4]
["Rv3849","TF",2,"Involved in transcriptional mechanism. Regulates transcription of genes required for ESX-1 system.",{"$nulls":4},1,12]
["Rv3855","TF",1,"Regulates negatively the production of ETHA. Induced ETH resistance when overexpressed in Mycobacterium tuberculosis.",{"$nulls":4},0,1]
["Rv3911","SF",1,"Possible alternative RNA polymerase sigma factor SigM",{"$nulls":4},0,91]

{"sheet":"CG","index":5,"n_rows":67,"n_cols":9,"rows_kept":67,"cut":false,"hidden":false,"merged":[[2,3,2,6]],"flags":["formulas_cached_only"]}
["Table 2E. Biological function of transcription factors and sigma factors of transcription regulatory network of C. glutamicum.  "]
[]
["Transcription factor","Type","Dominance level","Biological function ",null,null,null,"in degree","out degree"]
["AcnR","TF",4,"Tricarboxylic acid cycle",null,null,null,5,2]
["AmtR","TF",1,"Nitrogen metabolism",null,null,null,0,37]
["ArgR","TF",2,"Arginine biosynthesis",null,null,null,2,8]
["ArnR","TF",1,"Aerobic repressor of nitrate reductase R",null,null,null,1,7]
["ArsR1","TF",1,"Transcription regulator ArsR",null,null,null,0,3]
["ArsR2","TF",1,"Transcription regulator ArsR",null,null,null,0,2]
["BioQ","TF",1,"Biotin biosynthesis",null,null,null,0,6]
["Cg0019","TF",1,"Bacterial regulatory protein, LysR family",null,null,null,0,1]
["Cg0051","TF",1,"AraC-type DNA-binding domain-containing protein",null,null,null,0,3]
["Cg0454","TF",1,"Multidrug resistance",null,null,null,1,3]
["Cg0500","TF",1,"Aromatic amino acid metabolism",null,null,null,0,1]
["Cg0702","TF",1,"Transcription factor",null,null,null,0,1]
["Cg0979","TF",1,"Lipoprotein export",null,null,null,1,3]
["Cg0993","TF",1,"Sulfur metabolism",null,null,null,1,2]
["Cg1032","TF",1,"Cadmium resistance",null,null,null,1,2]
["Cg1053","TF",1,"Multidrug resistance",null,null,null,0,1]
["Cg1211","TF",1,"Metabolite transport",null,null,null,0,1]
["Cg1308","TF",1,"Transcriptional regulator",null,null,null,0,3]
["Cg1831","TF",1,"Iron homeostasis",null,null,null,0,3]
["Cg1846","TF",1,"Bacterial regulatory proteins, tetR family",null,null,null,1,4]
["Cg2268","TF",1,"Bacterial regulatory protein, LysR family",null,null,null,0,1]
["Cg2500","TF",1,"Bacterial regulatory proteins, ArsR family",null,null,null,1,2]
["Cg2894","TF",1,"Drug resistance",null,null,null,1,2]
["Cg2942","TF",2,"Bacterial regulatory proteins, AsnC family",null,null,null,1,1]
["Cg2965","TF",2,"AraC-type DNA-binding domain-containing proteins",null,null,null,1,1]
["Cg3082","TF",2,"Iron homeostasis",null,null,null,2,4]
["Cg3239","TF",1,"Metabolite transport",null,null,null,0,1]
["Cg3388","TF",2,"Bacterial regulatory proteins, IclR family",null,null,null,1,3]
["ClgR","TF",4,"Proteolysis",null,null,null,2,8]
["CspA","TF",1,"Cold shock protein CspA",null,null,null,0,1]
["CysR","TF",2,"Methionine biosynthesis",null,null,null,1,18]
["DtxR","TF",1,"Iron homeostasis",null,null,null,0,64]
["FarR","TF",1,"GntR-family transcription regulator",null,null,null,1,10]
["FruR","TF",2,"Fructose utilization",null,null,null,4,5]
["GlxR","TF",1,"cAMP-binding domain containing protein",null,null,null,1,150]
["GntR1","TF",1,"Gluconate utilization",null,null,null,0,10]
["GntR2","TF",1,"Gluconate utilization",null,null,null,0,10]
["HrcA","TF",1,"Heat shock response",null,null,null,0,3]
["HspR","TF",3,"Heat shock response",null,null,null,2,7]
["IolR","TF",1,"Predicted transcriptional regulator",null,null,null,0,10]
["LexA","TF",2,"SOS response",null,null,null,2,48]
["LldR","TF",1,"Lactate utilization",null,null,null,0,5]
["Lrp","TF",1,"Leucine responsive regulator",null,null,null,1,3]
["LtbR","TF",1,"Predicted transcriptional regulator",null,null,null,0,9]
["LysG","TF",1,"Amino acid efflux",null,null,null,0,1]
["McbR","TF",1,"Methionine biosynthesis",null,null,null,1,46]
["MtrA","TF",1,"Two component system response regulator",null,null,null,0,4]
["NagR","TF",2,"3-hydroxybenzoate degradation",null,null,null,1,5]
["NrdR","TF",3,"Deoxyribonucleotide biosynthesis",null,null,null,1,3]
["NrtR","TF",1,"NAD biosynthesis",null,null,null,1,4]
["PcaR","TF",1,"Protocatechuate degradation",null,null,null,1,12]
["PdxR","TF",1,"Pyridoxine biosynthesis",null,null,null,0,2]
["PhoR","TF",1,"Predicted transcriptional regulator",null,null,null,1,18]
["PrpR","TF",1,"Predicted transcriptional regulator",null,null,null,0,3]
["PyrR","TF",4,"Pyrimidine metabolism",null,null,null,2,4]
["RamA","TF",2,"Regulatory-like protein",null,null,null,2,18]
["RamB","TF",3,"Predicted transcriptional regulator",null,null,null,3,52]
["RbsR","TF",1,"Transcriptional regulator",null,null,null,1,5]
["Rel","TF",1,"Ribose utilization",null,null,null,0,7]
["RpiR","TF",1,"RpiR family transcriptional regulator",null,null,null,1,6]
["SugR","TF",1,"Transcriptional regulator of sugar metabolism",null,null,null,1,39]
["UreR","TF",1,"Bacterial regulatory protein, MarR family",null,null,null,0,7]
["UriR","TF",1,"Pyrimidine utilization",null,null,null,0,3]
["VanR","TF",1,"Vanillate utilization",null,null,null,2,3]

{"sheet":"SA","index":6,"n_rows":49,"n_cols":9,"rows_kept":49,"cut":false,"hidden":false,"merged":[[2,3,2,6]],"flags":["formulas_cached_only"]}
["Table 2F. Biological function of transcription factors and sigma factors of transcription regulatory network of S . aureus.  "]
[]
["Transcription factor","Type","Dominance level","Biological function ",null,null,null,"in degree","out degree"]
["AgrA","TF",1,"Virulence; Quorum sensing",null,null,null,0,4]
["ArcR","TF",2,"Arginine degradation",null,null,null,3,3]
["ArgR","TF",1,"Arginine biosynthesis; Arginine degradation",null,null,null,0,15]
["ArsR","TF",1,"Arsenic resistance",null,null,null,0,4]
["BglR","TF",1,"Beta-glucosides utilization",null,null,null,0,2]
["BirA","TF",1,"Biotin biosynthesis",null,null,null,0,10]
["BlaI","TF",1,"Beta-lactam resistance",null,null,null,0,2]
["CcpA","TF",1,"Carbon catabolism",null,null,null,0,121]
["CggR","TF",1,"Glycolysis",null,null,null,0,5]
["CodY","TF",1,"Amino acid metabolism",null,null,null,0,146]
["CtsR","TF",1,"Heat shock response",null,null,null,0,12]
["CymR","TF",1,"Cysteine metabolism",null,null,null,0,21]
["CzrA","TF",1,"Zinc resistance",null,null,null,0,1]
["FapR","TF",1,"Fatty acid biosynthesis",null,null,null,0,7]
["FruR","TF",2,"Fructose utilization",null,null,null,1,2]
["Fur","TF",3,"Iron homeostasis",null,null,null,1,47]
["GlnR","TF",2,"Nitrogen assimilation",null,null,null,1,2]
["GltC","TF",2,"Glutamate metabolism",null,null,null,1,2]
["GlvR","TF",2,"Maltose utilization",null,null,null,1,1]
["GntR","TF",2,"Gluconate utilization",null,null,null,1,2]
["HisR","TF",1,"Histidine biosynthesis",null,null,null,0,12]
["HrcA","TF",2,"Heat shock response",null,null,null,1,5]
["HssR","TF",1,"Heme efflux",null,null,null,0,2]
["HutR","TF",1,"Histidine utilization",null,null,null,0,3]
["LacR","TF",1,"Lactose utilization",null,null,null,0,7]
["LcaR","TF",1,"Transcriptional regulator",null,null,null,0,4]
["LexA","TF",1,"SOS response",null,null,null,0,15]
["MalR","TF",2,"Maltose utilization",null,null,null,1,8]
["ManR","TF",2,"Mannose utilization",null,null,null,1,2]
["MecI","TF",1,"Penicillin and methicillin resistance",null,null,null,0,2]
["MepR","TF",1,"Multidrug resistance",null,null,null,0,1]
["MntR","TF",1,"Manganese homeostasis",null,null,null,0,4]
["MtlR","TF",1,"Mannitol utilization",null,null,null,0,3]
["MurR","TF",2,"N-acetylmuramate utilization",null,null,null,1,3]
["NrdR","TF",1,"Deoxyribonucleotide biosynthesis",null,null,null,0,5]
["NreC","TF",2,"Nitrate and nitrite respiration",null,null,null,1,12]
["PdxR","TF",1,"Pyridoxine biosynthesis",null,null,null,0,2]
["PerR","TF",2,"Oxidative stress response",null,null,null,1,15]
["PurR","TF",1,"Purine metabolism",null,null,null,0,14]
["RbsR","TF",1,"Ribose utilization",null,null,null,0,3]
["Rex","TF",1,"Energy metabolism",null,null,null,0,38]
["SaeR","TF",1,"Virulence",null,null,null,0,30]
["ScrR","TF",2,"Sucrose utilization",null,null,null,1,3]
["TreR","TF",2,"Trehalose utilization",null,null,null,1,2]
["YtrA","TF",1,"Hypothetical ABC transporter",null,null,null,0,4]
["Zur","TF",1,"Zinc homeostasis",null,null,null,0,11]