Organism : Bacillus subtilis | Module List :
Regulation information for BSU28060(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 BSU28060
|Gene||Common Name||Description||Module membership|
|BSU01530||cwlD||N-acetylmuramoyl-L-alanine amidase (RefSeq)||33, 304|
|BSU01910||skfA||sporulation killing factor A (RefSeq)||33, 141|
|BSU01920||skfB||synthesis of sporulation killing factor A (RefSeq)||33, 141|
|BSU01950||skfE||sporulation killing factor biosynthesis and export; ABC transporter (binding protein) (RefSeq)||8, 33|
|BSU01960||skfF||sporulation killing factor biosynthesis and export; ABC transporter (permease) (RefSeq)||33, 141|
|BSU01970||skfG||sporulation killing factor biosynthesis and export (RefSeq)||8, 33|
|BSU06920||yesJ||putative acetyltransferase (RefSeq)||33, 156|
|BSU06930||yesK||putative permease (RefSeq)||33, 156|
|BSU07130||lplD||putative glycosidase (RefSeq)||33, 129|
|BSU07270||yfnH||putative sugar-phosphate cytidylyltransferase (RefSeq)||156, 277|
|BSU07280||yfnG||putative CDP-sugar-dehydratase/epimerase (RefSeq)||277, 281|
|BSU07290||yfnF||putative glycosyltransferase (RefSeq)||277, 281|
|BSU07300||yfnE||putative glycosyltransferase (complex carbohydrate synthase) (RefSeq)||277, 281|
|BSU07840||yfkN||bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein (RefSeq)||33, 174|
|BSU08070||acoB||acetoin dehydrogenase E1 component (TPP-dependent beta subunit) (RefSeq)||17, 277|
|BSU08080||acoC||branched-chain alpha-keto acid dehydrogenase subunit E2 (RefSeq)||17, 277|
|BSU08090||acoL||dihydrolipoamide dehydrogenase (RefSeq)||17, 277|
|BSU08100||acoR||transcriptional regulator (RefSeq)||277, 321|
|BSU08110||sspH||acid-soluble spore protein H (RefSeq)||33, 133|
|BSU08670||ygaB||hypothetical protein (RefSeq)||33, 278|
|BSU10960||yitE||putative integral inner membrane protein (RefSeq)||277, 286|
|BSU11790||yjcA||sporulation-specific protein (RefSeq)||108, 277|
|BSU12320||yjmC||putative oxidoreductase (RefSeq)||26, 33|
|BSU12330||yjmD||putative oxidoreductase (RefSeq)||26, 33|
|BSU12340||uxuA||mannonate dehydratase (RefSeq)||26, 33|
|BSU12350||yjmF||D-mannonate oxidoreductase (RefSeq)||26, 33|
|BSU12360||exuT||hexuronate transporter (RefSeq)||33, 329|
|BSU13290||ykzD||hypothetical protein (RefSeq)||8, 277|
|BSU13830||ykvU||spore membrane protein involved in germination (RefSeq)||277, 286|
|BSU13840||stoA||thiol-disulfide isomerase (RefSeq)||277, 286|
|BSU22280||yppD||hypothetical protein (RefSeq)||25, 33|
|BSU22570||ypiF||hypothetical protein (RefSeq)||33, 340|
|BSU23440||spoVAA||stage V sporulation protein AA (RefSeq)||277, 367|
|BSU24510||yqhO||hypothetical protein (RefSeq)||33, 86|
|BSU25750||nucB||nuclease (RefSeq)||33, 278|
|BSU25760||spoIVCB||RNA polymerase sporulation-specific sigma factor (sigma-K) (N-terminal half) (RefSeq)||33, 127|
|BSU25820||yqcI||hypothetical protein (RefSeq)||277, 282|
|BSU27690||yrzE||putative integral inner membrane protein (RefSeq)||277, 286|
|BSU27980||spoIVFA||regulator of SpoIVFB (stage IV sporulation) (RefSeq)||277, 286|
|BSU28060||spoIIB||spatial and temporal regulator of the dissolution of septal peptidoglycan during engulfment (stage II sporulation) (RefSeq)||33, 277|
|BSU37480||ywhH||putative RNA-binding protein (RefSeq)||33, 350|
|BSU38230||ywcB||putative phage protein (superinfection immunity) (RefSeq)||33, 411|
|BSU38240||ywcA||putative acetate Na+-dependent symporter (RefSeq)||33, 250|
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.
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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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- 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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