Organism : Bacillus subtilis | Module List :
Regulation information for BSU12510(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Functional Enrichment for BSU12510
Module neighborhood information for BSU12510
|Gene||Common Name||Description||Module membership|
|BSU01000||secE||preprotein translocase subunit SecE (RefSeq)||191, 226|
|BSU03670||dtpT||di-tripeptide-proton ABC symporter (RefSeq)||258, 315|
|BSU03750||yclJ||two-component response regulator [YclK] (RefSeq)||37, 258|
|BSU03760||yclK||two-component sensor histidine kinase [YclJ] (RefSeq)||37, 258|
|BSU04770||ydcH||putative transcriptional regulator (RefSeq)||151, 258|
|BSU05620||ydgF||putative amino acid permease (RefSeq)||226, 258|
|BSU07330||yfnB||putative hydrolase (RefSeq)||215, 258|
|BSU07390||yfmP||transcriptional regulator (MerR family) of metal efflux transporter expression (RefSeq)||161, 258|
|BSU08020||yfjO||putative RNA methyltransferase (RefSeq)||170, 191|
|BSU08340||padR||transcriptional regulator (RefSeq)||216, 258|
|BSU08520||recX||recombination regulator RecX (RefSeq)||94, 258|
|BSU09610||yhdV||integral membrane protein possibly involved in chromosome condensation (RefSeq)||94, 258|
|BSU09620||yhdW||putative glycerophosphodiester phosphodiesterase (RefSeq)||23, 258|
|BSU12370||exuR||transcriptional regulator (LacI family) (RefSeq)||35, 191|
|BSU12510||xre||Phage PBSX transcriptional regulator (RefSeq)||191, 258|
|BSU13310||tnrA||nitrogen sensing transcriptional regulator (RefSeq)||216, 258|
|BSU14420||ykoA||hypothetical protein (RefSeq)||219, 258|
|BSU14430||ykpA||ABC efflux transporter (ATP-binding protein) (RefSeq)||142, 258|
|BSU14830||ylaM||glutaminase (RefSeq)||258, 323|
|BSU17080||pksA||putative transcriptional regulator (RefSeq)||191, 258|
|BSU17730||yndB||hypothetical protein (RefSeq)||258, 323|
|BSU19340||yocR||putative sodium-dependent transporter (RefSeq)||116, 191|
|BSU21790||yplQ||putative membrane hydrolase (RefSeq)||51, 191|
|BSU22980||ypbG||putative phosphoesterase (RefSeq)||94, 258|
|BSU23250||ribH||6,7-dimethyl-8-ribityllumazine synthase (RefSeq)||97, 191|
|BSU23260||ribA||bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein (RefSeq)||97, 191|
|BSU23270||ribE||riboflavin synthase subunit alpha (RefSeq)||97, 191|
|BSU23280||ribD||fused diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino) uracil reductase (RefSeq)||97, 191|
|BSU23380||lysA||diaminopimelate decarboxylase (RefSeq)||191, 322|
|BSU23570||aspA||aspartate ammonia-lyase (RefSeq)||258, 293|
|BSU23580||ansA||exported L-asparaginase (RefSeq)||258, 293|
|BSU23590||ansR||transcriptional regulator of ansAB (Xre family) (RefSeq)||151, 258|
|BSU25130||yqfS||endonuclease IV (RefSeq)||191, 204|
|BSU25210||dnaG||DNA primase (RefSeq)||191, 309|
|BSU25280||recO||DNA repair protein RecO (RefSeq)||97, 191|
|BSU27800||yrzH||hypothetical protein (RefSeq)||64, 258|
|BSU27910||pheB||hypothetical protein (RefSeq)||191, 221|
|BSU30310||ytwF||putative sulfur transferase (RefSeq)||258, 323|
|BSU30480||ytqA||putative Fe-S oxidoreductase (RefSeq)||191, 265|
|BSU32170||dapF||diaminopimelate epimerase (RefSeq)||164, 258|
|BSU32420||pucR||transcriptional regulator of the purine degradation operon (RefSeq)||257, 258|
|BSU32740||metP||methionine ABC transporter, permease component (RefSeq)||139, 191|
|BSU32750||metQ||methionine ABC transporter (ATP-binding protein) (RefSeq)||139, 191|
|BSU33110||liaG||conserved hypothetical protein (response to antibiotic stress) (RefSeq)||23, 191|
|BSU33370||yvgK||putative molybdate binding regulator (RefSeq)||164, 258|
|BSU33660||rghRA||transcriptional repressor (RefSeq)||49, 258|
|BSU33670||rghRB||putative transcriptional repressor (RefSeq)||49, 258|
|BSU33680||yvaP||putative transcriptional regulator (RefSeq)||49, 258|
|BSU33780||sdpI||integral inner membrane regulator of autophagy (RefSeq)||191, 258|
|BSU33790||sdpR||transcriptional regulator (ArsR family) (RefSeq)||191, 258|
|BSU34420||yveF||hypothetical protein (RefSeq)||174, 258|
|BSU40470||yycC||hypothetical protein (RefSeq)||159, 191|
|BSU40480||yycB||putative anion ABC transporter (permease) (RefSeq)||159, 191|
|BSU40990||noc||DNA-binding protein Spo0J-like (RefSeq)||191, 228|
Gene Page Help
If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.
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Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.
If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
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Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.
Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
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Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.
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CircVisOur circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
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