Organism : Bacillus subtilis | Module List :
Regulation information for BSU26240(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 BSU26240
|Gene||Common Name||Description||Module membership|
|BSU00990||rpmG||50S ribosomal protein L33 (RefSeq)||64, 200|
|BSU03100||ycgG||hypothetical protein (RefSeq)||216, 291|
|BSU03450||hxlB||6-phospho-3-hexuloisomerase (PHI) (RefSeq)||64, 296|
|BSU03460||hxlA||3-hexulose-6-phosphate synthase (HPS) (RefSeq)||64, 296|
|BSU04020||yczH||putative hydrolase (RefSeq)||64, 145|
|BSU05150||ydeC||putative transcriptional regulator (AraC/XylS family) (RefSeq)||157, 216|
|BSU05180||ydeF||putative PLP-dependent transcriptional regulator (RefSeq)||115, 216|
|BSU05600||ydgE||putative N-acetyltransferase (RefSeq)||111, 216|
|BSU07220||yetL||putative transcriptional regulator (MarR family) (RefSeq)||216, 378|
|BSU08340||padR||transcriptional regulator (RefSeq)||216, 258|
|BSU09540||plsC||1-acylglycerol-phosphate (1-acyl-G3P) acyltransferase (RefSeq)||64, 404|
|BSU09600||crcBA||camphor resistance protein CrcB (RefSeq)||64, 115|
|BSU10010||trpP||tryptophan transporter (RefSeq)||64, 94|
|BSU10880||yisV||putative PLP-dependent transcriptional regulator (RefSeq)||64, 318|
|BSU10990||yitH||putative N-acetyltransferase (RefSeq)||64, 171|
|BSU11000||yitI||putative N-acetyltransferase (RefSeq)||64, 219|
|BSU11270||yjzD||hypothetical protein (RefSeq)||64, 157|
|BSU11280||yjaU||hypothetical protein (RefSeq)||64, 157|
|BSU11480||yjbB||putative exporter (RefSeq)||64, 350|
|BSU11510||yjbE||putative transporter component (RefSeq)||64, 115|
|BSU11890||yjcK||putative ribosomal-protein-alanine N-acetyltransferase (RefSeq)||157, 216|
|BSU12060||yjdI||hypothetical protein (RefSeq)||49, 216|
|BSU12500||xkdA||PBSX phage protein, putative peptidase (RefSeq)||64, 96|
|BSU13070||ykkA||hypothetical protein (RefSeq)||64, 171|
|BSU13080||ykkB||putative N-acetyltransferase (RefSeq)||64, 171|
|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|
|BSU15420||divIVA||cell-division initiation protein (RefSeq)||64, 402|
|BSU18620||yoaI||putative 4-hydroxyphenylacetate-3-hydroxylase (RefSeq)||64, 379|
|BSU18690||yoaP||hypothetical protein (RefSeq)||64, 129|
|BSU18730||yoaS||hypothetical protein (RefSeq)||216, 327|
|BSU18750||yoaT||putative integral inner membrane protein (RefSeq)||216, 327|
|BSU19090||yobU||putative effector of transcriptional regulator (RefSeq)||64, 239|
|BSU19100||yobV||putative transcriptional regulator (RefSeq)||64, 170|
|BSU21830||ypjQ||putative phosphatidylglycerophosphatase (RefSeq)||64, 404|
|BSU22010||exoA||5'3'-exonuclease (RefSeq)||216, 226|
|BSU22300||yppC||hypothetical protein (RefSeq)||216, 308|
|BSU22970||ypbH||adaptor protein (RefSeq)||51, 216|
|BSU26230||yqaP||conserved hypothetical protein; skin element (RefSeq)||25, 64|
|BSU26240||yqaO||conserved hypothetical protein; skin element (RefSeq)||64, 216|
|BSU26550||yrkD||hypothetical protein (RefSeq)||51, 216|
|BSU26630||yrdQ||putative transcriptional regulator (LysR family) (RefSeq)||216, 226|
|BSU27110||yrhO||putative transcriptional regulator (RefSeq)||216, 378|
|BSU27800||yrzH||hypothetical protein (RefSeq)||64, 258|
|BSU27810||yrbD||sodium/proton-dependent alanine transporter (RefSeq)||64, 304|
|BSU28600||yshB||putative integral inner membrane protein (RefSeq)||216, 226|
|BSU30670||luxS||S-ribosylhomocysteinase (RefSeq)||49, 64|
|BSU30680||ytjA||hypothetical protein (RefSeq)||64, 115|
|BSU31130||yubD||putative efflux transporter (RefSeq)||66, 216|
|BSU31580||maeN||Na+/malate symporter (RefSeq)||64, 238|
|BSU33030||yuxN||putative transcriptional regulator (RefSeq)||151, 216|
|BSU35740||tagD||glycerol-3-phosphate cytidylyltransferase (RefSeq)||216, 226|
|BSU35880||pgsA||capsular polyglutamate synthetase (RefSeq)||64, 318|
|BSU36160||ywqM||putative transcriptional regulator (LysR family) (RefSeq)||49, 216|
|BSU36320||ywpG||hypothetical protein (RefSeq)||64, 318|
|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|
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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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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