Organism : Bacillus subtilis | Module List :
Regulation information for VIMSS36736(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|
Module neighborhood information for VIMSS36736
|Gene||Common Name||Description||Module membership|
|BSU01000||secE||preprotein translocase subunit SecE (RefSeq)||191, 226|
|BSU08020||yfjO||putative RNA methyltransferase (RefSeq)||170, 191|
|BSU10410||yhzC||hypothetical protein (RefSeq)||249, 381|
|BSU12370||exuR||transcriptional regulator (LacI family) (RefSeq)||35, 191|
|BSU12510||xre||Phage PBSX transcriptional regulator (RefSeq)||191, 258|
|BSU13700||clpE||ATP-dependent Clp protease (class III stress gene) (RefSeq)||249, 379|
|BSU13760||ykvN||putative transcriptional regulator (RefSeq)||109, 249|
|BSU13850||zosA||Zn transporter (RefSeq)||111, 249|
|BSU17080||pksA||putative transcriptional regulator (RefSeq)||191, 258|
|BSU19340||yocR||putative sodium-dependent transporter (RefSeq)||116, 191|
|BSU21680||yppQ||methionine sulfoxide reductase B (RefSeq)||249, 373|
|BSU21690||msrA||methionine sulfoxide reductase A (RefSeq)||249, 373|
|BSU21790||yplQ||putative membrane hydrolase (RefSeq)||51, 191|
|BSU22580||ypiB||hypothetical protein (RefSeq)||249, 340|
|BSU22590||ypiA||hypothetical protein (RefSeq)||249, 340|
|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|
|BSU23520||fur||transcriptional regulator for iron transport and metabolism (RefSeq)||49, 249|
|BSU24950||pstBB||phosphate ABC transporter ATP-binding protein (RefSeq)||249, 349|
|BSU24960||pstBA||phosphate ABC transporter ATP-binding protein (RefSeq)||249, 349|
|BSU24970||pstA||phosphate ABC transporter (permease) (RefSeq)||249, 349|
|BSU24980||pstC||phosphate ABC transporter (permease) (RefSeq)||249, 349|
|BSU24990||pstS||phosphate ABC transporter (binding lipoprotein) (RefSeq)||249, 349|
|BSU25130||yqfS||endonuclease IV (RefSeq)||191, 204|
|BSU25210||dnaG||DNA primase (RefSeq)||191, 309|
|BSU25280||recO||DNA repair protein RecO (RefSeq)||97, 191|
|BSU25780||arsC||arsenate reductase (RefSeq)||161, 249|
|BSU25790||arsB||arsenite efflux transporter (RefSeq)||49, 249|
|BSU25800||yqcK||putative thiol lyase (RefSeq)||49, 249|
|BSU25810||arsR||transcriptional regulator (ArsR family) (RefSeq)||49, 249|
|BSU27910||pheB||hypothetical protein (RefSeq)||191, 221|
|BSU30020||ytzE||putative transcriptional regulator (DeoR family) (RefSeq)||91, 249|
|BSU30480||ytqA||putative Fe-S oxidoreductase (RefSeq)||191, 265|
|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|
|BSU33490||copB||copper(I)-transporting ATPase (RefSeq)||161, 249|
|BSU33780||sdpI||integral inner membrane regulator of autophagy (RefSeq)||191, 258|
|BSU33790||sdpR||transcriptional regulator (ArsR family) (RefSeq)||191, 258|
|BSU34480||yvdT||putative transcriptional regulator (TetR/AcrR family) (RefSeq)||249, 393|
|BSU39250||yxiE||phosphate starvation protein (universal stress protein A family) (RefSeq)||249, 381|
|BSU40470||yycC||hypothetical protein (RefSeq)||159, 191|
|BSU40480||yycB||putative anion ABC transporter (permease) (RefSeq)||159, 191|
|BSU40540||yybR||putative transcriptional regulator (RefSeq)||109, 249|
|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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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.
Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.
Module Members Tab
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;
- 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
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