Organism : Bacillus subtilis | Module List :
Regulation information for BSU13320(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 BSU13320
|Gene||Common Name||Description||Module membership|
|BSU01730||sigW||RNA polymerase sigma factor SigW (RefSeq)||159, 166|
|BSU01740||rsiW||anti-sigma(W) factor (RefSeq)||159, 166|
|BSU03100||ycgG||hypothetical protein (RefSeq)||216, 291|
|BSU05120||cspC||cold-shock protein (RefSeq)||151, 159|
|BSU05150||ydeC||putative transcriptional regulator (AraC/XylS family) (RefSeq)||157, 216|
|BSU05180||ydeF||putative PLP-dependent transcriptional regulator (RefSeq)||115, 216|
|BSU05200||ydeH||putative integral inner membrane protein (RefSeq)||115, 159|
|BSU05600||ydgE||putative N-acetyltransferase (RefSeq)||111, 216|
|BSU06270||ydjO||hypothetical protein (RefSeq)||159, 266|
|BSU07220||yetL||putative transcriptional regulator (MarR family) (RefSeq)||216, 378|
|BSU08340||padR||transcriptional regulator (RefSeq)||216, 258|
|BSU11300||med||positive regulator of comK (RefSeq)||14, 159|
|BSU11890||yjcK||putative ribosomal-protein-alanine N-acetyltransferase (RefSeq)||157, 216|
|BSU11920||yjcN||hypothetical protein (RefSeq)||36, 159|
|BSU11930||yjcO||putative DNA binding protein (RefSeq)||36, 159|
|BSU12040||yjdG||putative acetyltransferase (RefSeq)||49, 159|
|BSU12060||yjdI||hypothetical protein (RefSeq)||49, 216|
|BSU13310||tnrA||nitrogen sensing transcriptional regulator (RefSeq)||216, 258|
|BSU13320||ykzB||hypothetical protein (RefSeq)||159, 216|
|BSU13770||ykvO||putative oxidoreductase (RefSeq)||44, 216|
|BSU13800||ykvR||hypothetical protein (RefSeq)||109, 216|
|BSU13820||ykvT||cell wall hydrolase related to spore cortex-lytic enzymes (RefSeq)||116, 216|
|BSU14990||ylbF||putative regulatory protein (RefSeq)||159, 170|
|BSU17060||ymzD||putative integral inner membrane protein (RefSeq)||115, 159|
|BSU17230||pksS||cytochrome P450 of bacillaene metabolism (RefSeq)||36, 159|
|BSU18650||pelB||pectin lyase (RefSeq)||159, 179|
|BSU18730||yoaS||hypothetical protein (RefSeq)||216, 327|
|BSU18750||yoaT||putative integral inner membrane protein (RefSeq)||216, 327|
|BSU18980||yobJ||hypothetical protein (RefSeq)||159, 166|
|BSU21780||yplP||transcriptional enhancer (RefSeq)||159, 226|
|BSU22010||exoA||5'3'-exonuclease (RefSeq)||216, 226|
|BSU22300||yppC||hypothetical protein (RefSeq)||216, 308|
|BSU22970||ypbH||adaptor protein (RefSeq)||51, 216|
|BSU23090||rsiX||negative regulator of sigma(X) activity (RefSeq)||145, 159|
|BSU23100||sigX||RNA polymerase sigma factor SigX (RefSeq)||145, 159|
|BSU23310||sipS||type I signal peptidase (RefSeq)||94, 159|
|BSU23720||yqzH||hypothetical protein (RefSeq)||159, 270|
|BSU23730||yqjV||putative efflux transporter (RefSeq)||36, 159|
|BSU25090||yqfW||putative nucleotidase (RefSeq)||151, 159|
|BSU25560||holA||DNA polymerase III subunit delta (RefSeq)||151, 159|
|BSU25690||sda||check point factor coupling initiation of sporulation and replication initiation (RefSeq)||36, 159|
|BSU25700||yqeF||putative lipoprotein; putative esterase (RefSeq)||121, 159|
|BSU26240||yqaO||conserved hypothetical protein; skin element (RefSeq)||64, 216|
|BSU26550||yrkD||hypothetical protein (RefSeq)||51, 216|
|BSU26610||yrkA||putative membrane associated protein (RefSeq)||159, 170|
|BSU26630||yrdQ||putative transcriptional regulator (LysR family) (RefSeq)||216, 226|
|BSU27110||yrhO||putative transcriptional regulator (RefSeq)||216, 378|
|BSU28600||yshB||putative integral inner membrane protein (RefSeq)||216, 226|
|BSU31130||yubD||putative efflux transporter (RefSeq)||66, 216|
|BSU33030||yuxN||putative transcriptional regulator (RefSeq)||151, 216|
|BSU35740||tagD||glycerol-3-phosphate cytidylyltransferase (RefSeq)||216, 226|
|BSU35840||ywtF||putative transcriptional regulator (RefSeq)||159, 170|
|BSU36160||ywqM||putative transcriptional regulator (LysR family) (RefSeq)||49, 216|
|BSU36440||ywoH||putative transcriptional regulator (MarR family) (RefSeq)||51, 216|
|BSU36450||ywoG||putative efflux transporter (RefSeq)||51, 216|
|BSU36980||ywlA||putative integral inner membrane protein (RefSeq)||216, 378|
|BSU39010||yxjB||putative ribosomal RNA methyltransferase (RefSeq)||51, 159|
|BSU39240||yxxF||putative transporter (RefSeq)||159, 350|
|BSU40470||yycC||hypothetical protein (RefSeq)||159, 191|
|BSU40480||yycB||putative anion ABC transporter (permease) (RefSeq)||159, 191|
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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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.
- 2. Source gene
- 3. Target genes (other module members)
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