Organism : Bacillus subtilis | Module List :
Regulation information for BSU04110(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 BSU04110
Module neighborhood information for BSU04110
|Gene||Common Name||Description||Module membership|
|BSU02260||ybfK||carboxylesterase NP (RefSeq)||11, 155|
|BSU02710||yczC||putative integral inner membrane protein (RefSeq)||96, 307|
|BSU02800||ycdC||putative hydrolase (RefSeq)||11, 202|
|BSU03070||mdr||multidrug-efflux transporter (RefSeq)||11, 339|
|BSU03220||ycgO||putative proline/ornithine permease (RefSeq)||11, 261|
|BSU03340||yciA||putative GTP cyclohydrolase (RefSeq)||307, 406|
|BSU03790||yclM||aspartate kinase (RefSeq)||11, 365|
|BSU03850||ycnC||putative transcriptional regulator (TetR/AcrR family) (RefSeq)||11, 13|
|BSU04110||lipC||lysophopholipase (RefSeq)||11, 307|
|BSU05440||nap||carboxylesterase NP (RefSeq)||11, 341|
|BSU06870||yesE||hypothetical protein (RefSeq)||307, 361|
|BSU08230||catD||catechol-2,3-dioxygenase membrane subunit (RefSeq)||178, 307|
|BSU08240||catE||catechol-2,3-dioxygenase subunit (RefSeq)||238, 307|
|BSU08290||yfiJ||two-component sensor histidine kinase [YfiK] (RefSeq)||132, 307|
|BSU08300||yfiK||two-component response regulator [YfiJ] (RefSeq)||48, 307|
|BSU09050||yhcE||putative integral inner membrane orphan protein (RefSeq)||11, 339|
|BSU09060||yhcF||putative transcriptional regulator (GntR family) (RefSeq)||11, 102|
|BSU09070||yhcG||putative ABC transporter ATP-binding protein (RefSeq)||11, 339|
|BSU10170||fabHB||3-oxoacyl-(acyl carrier protein) synthase III (RefSeq)||307, 411|
|BSU11040||yitM||hypothetical protein (RefSeq)||217, 307|
|BSU11320||yjzB||hypothetical protein (RefSeq)||307, 411|
|BSU14200||ykuS||hypothetical protein (RefSeq)||11, 365|
|BSU19050||yobQ||putative transcriptional regulator (AraC/XylS family) (RefSeq)||11, 261|
|BSU19060||yobR||putative acetyltransferase (RefSeq)||11, 261|
|BSU19070||yobS||putative transcriptional regulator (RefSeq)||11, 327|
|BSU21310||yozP||hypothetical protein; phage SPbeta (RefSeq)||174, 307|
|BSU21530||yolB||conserved hypothetical protein; phage SPbeta (RefSeq)||298, 307|
|BSU21540||yolA||exported protein of unknown function; phage SPbeta (RefSeq)||298, 307|
|BSU23670||yqkA||hypothetical protein (RefSeq)||11, 79|
|BSU23690||yqjY||putative acetyltransferase (RefSeq)||11, 79|
|BSU24100||bkdR||transcriptional regulator (RefSeq)||11, 261|
|BSU26740||cypA||cytochrome P450 (RefSeq)||280, 307|
|BSU31440||patB||C-S lyase (RefSeq)||11, 128|
|BSU32070||yuiC||hypothetical protein (RefSeq)||291, 307|
|BSU32650||yurS||hypothetical protein (RefSeq)||280, 307|
|BSU33350||yvsG||putative membrane hydrolase (RefSeq)||11, 319|
|BSU34000||cyeB||cysteine and O-acetylserine efflux permease (RefSeq)||96, 307|
|BSU35280||yvjA||putative integral inner membrane protein (RefSeq)||307, 411|
|BSU35770||tagC||putative polyglycerol phosphate assembly and export protein (teichoic acid biosynthesis) (RefSeq)||239, 307|
|BSU36480||ywoD||putative efflux transporter (RefSeq)||50, 307|
|BSU36490||ywoC||putative hydrolase (RefSeq)||50, 307|
|BSU36500||ywoB||putative integral inner membrane protein (RefSeq)||130, 307|
|BSU37560||thrZ||threonyl-tRNA synthetase (RefSeq)||11, 300|
|BSU38250||ywbO||putative sulfur oxido-reductase (RefSeq)||96, 307|
|BSU38910||yxjL||two-component response regulator [YxjM] (RefSeq)||11, 233|
|BSU39960||yxaI||putative integral inner membrane protein (RefSeq)||11, 13|
|BSU40670||yybE||putative transcriptional regulator (LysR family) (RefSeq)||11, 240|
|BSU40680||yybD||putative acetyltransferase (RefSeq)||11, 240|
|BSU40690||yybC||putative integral inner membrane protein (RefSeq)||11, 402|
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.
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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