Organism : Bacillus subtilis | Module List :
Regulation information for BSU14710(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 BSU14710
|Gene||Common Name||Description||Module membership|
|BSU01990||ybdG||putative hydrolase/transferase (RefSeq)||89, 360|
|BSU02440||glnJ||two-component sensor histidine kinase [GlnL] for glutamine degradation (RefSeq)||318, 361|
|BSU02950||yceI||putative transporter (RefSeq)||89, 365|
|BSU03250||ycgR||putative permease (RefSeq)||89, 233|
|BSU04440||dctB||C4-dicarboxylate binding protein (RefSeq)||246, 361|
|BSU04450||dctS||two-component sensor histidine kinase (RefSeq)||246, 361|
|BSU04460||dctR||two-component response regulator (RefSeq)||246, 361|
|BSU04500||ydbK||putative efflux ABC-transporter (permease component) (RefSeq)||89, 240|
|BSU06860||yezE||putative transcriptional regulator (TetR family) (RefSeq)||233, 361|
|BSU06870||yesE||hypothetical protein (RefSeq)||307, 361|
|BSU06880||yesF||hypothetical protein (RefSeq)||10, 361|
|BSU08040||yfjM||hypothetical protein (RefSeq)||102, 361|
|BSU09890||natA||Na+-efflux ABC transporter (ATP-binding protein) (RefSeq)||89, 313|
|BSU09900||natB||Na+ exporter (ABC permease) (RefSeq)||89, 313|
|BSU10640||sbcD||DNA repair exonuclease (RefSeq)||50, 361|
|BSU10650||sbcC||DNA ATP-dependent repair enzyme (RefSeq)||50, 361|
|BSU10660||yisB||putative nuclease component (RefSeq)||50, 361|
|BSU11180||yitZ||putative transport protein (RefSeq)||89, 313|
|BSU12480||yjqB||putative PBSX phage-related replication protein (RefSeq)||89, 202|
|BSU13430||ykoX||putative integral inner membrane protein (RefSeq)||38, 89|
|BSU13890||ptsG||phosphotransferase system (PTS) glucose-specific enzyme IICBA component (RefSeq)||89, 138|
|BSU14710||ylaA||hypothetical protein (RefSeq)||89, 361|
|BSU14720||ylaB||hypothetical protein (RefSeq)||89, 231|
|BSU14740||ylaD||anti-YlaC sigma factor (RefSeq)||231, 361|
|BSU15460||rluD||pseudouridylate synthase (RefSeq)||62, 89|
|BSU24880||yqgO||hypothetical protein (RefSeq)||89, 202|
|BSU24890||yqgN||5-formyltetrahydrofolate cyclo-ligase (RefSeq)||89, 385|
|BSU26680||yrdK||hypothetical protein (RefSeq)||89, 270|
|BSU32530||yurH||allantoate amidohydrolase (RefSeq)||89, 318|
|BSU34010||yvbW||putative amino acid permease (RefSeq)||322, 361|
|BSU34060||yvfU||two-component response regulator [YvfT] (RefSeq)||318, 361|
|BSU34070||yvfT||two-component sensor histidine kinase [YvfU] (RefSeq)||318, 361|
|BSU34450||sacB||levansucrase (RefSeq)||40, 89|
|BSU34960||yvoF||putative O-acetyltransferase (RefSeq)||106, 361|
|BSU34970||hprP||pyrophosphatase PpaX (RefSeq)||106, 361|
|BSU34980||yvoD||putative integral inner membrane protein (RefSeq)||106, 361|
|BSU34990||lgt||prolipoprotein diacylglyceryl transferase (RefSeq)||106, 361|
|BSU35000||hprK||HPr kinase/phosphorylase (RefSeq)||106, 361|
|BSU35010||nagA||N-acetylglucosamine-6-phosphate deacetylase (RefSeq)||334, 361|
|BSU35020||nagBA||N-acetylglucosamine-6-phosphate isomerase (RefSeq)||334, 361|
|BSU36470||pucI||allantoin permease (RefSeq)||84, 89|
|BSU37060||tdk||thymidine kinase (RefSeq)||89, 142|
|BSU38710||yxlA||putative purine-cytosine permease (RefSeq)||89, 177|
|BSU38900||yxjM||two-component sensor histidine kinase [YxjL] (RefSeq)||89, 233|
|BSU39620||yxeA||hypothetical protein (RefSeq)||89, 208|
|BSU39630||yxdM||ABC transporter (permease); efflux of cationic peptides (RefSeq)||84, 89|
|BSU39640||yxdL||ABC transporter (ATP-binding protein); efflux of cationic peptides (RefSeq)||84, 89|
|BSU39650||yxdK||two-component sensor histidine kinase [YxdJ] (RefSeq)||89, 361|
|BSU39660||yxdJ||two-component response regulator [YxdK] (RefSeq)||89, 361|
|BSU40880||exoAA||apurinic/apyrimidinic endonuclease (RefSeq)||89, 301|
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.
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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;
- 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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