Organism : Bacillus subtilis | Module List :
Regulation information for BSU21980(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 BSU21980
Module neighborhood information for BSU21980
|Gene||Common Name||Description||Module membership|
|BSU01800||alkA||DNA-3-methyladenine glycosylase (RefSeq)||115, 157|
|BSU01810||adaA||methylphosphotriester-DNA alkyltransferase and transcriptional regulator (AraC/XylS family) (RefSeq)||157, 406|
|BSU03020||ycgA||putative integral inner membrane protein (RefSeq)||157, 161|
|BSU05060||lrpB||transcriptional regulator (Lrp/AsnC family) (RefSeq)||115, 157|
|BSU05150||ydeC||putative transcriptional regulator (AraC/XylS family) (RefSeq)||157, 216|
|BSU05170||ydeE||putative transcriptional regulator (AraC/XylS family) (RefSeq)||115, 157|
|BSU05210||ydeI||hypothetical protein (RefSeq)||115, 157|
|BSU05460||ydfL||putative transcriptional regulator of efflux transporter (RefSeq)||115, 157|
|BSU06000||ydiK||hypothetical protein (RefSeq)||39, 311|
|BSU06800||yezA||hypothetical protein (RefSeq)||129, 311|
|BSU07320||yfnC||putative efflux transporter (RefSeq)||86, 311|
|BSU07970||yfjT||hypothetical protein (RefSeq)||94, 157|
|BSU08780||ygaJ||putative peptidase (RefSeq)||285, 311|
|BSU09380||nsrR||NO-dependent activator of the ResDE regulon (RefSeq)||222, 311|
|BSU09460||ctrA||branched-chain amino acid transporter (RefSeq)||38, 311|
|BSU10450||yhjB||putative Na+/metabolite cotransporter (RefSeq)||71, 311|
|BSU10460||yhjC||hypothetical protein (RefSeq)||285, 311|
|BSU10520||glcP||glucose/mannose:H+ symporter (RefSeq)||310, 311|
|BSU10530||ntdC||biosynthesis of neotrehalosadiamine (3,3'-diamino-3,3'-dideoxy-alpha,beta-trehalose), dehydrogenase (RefSeq)||310, 311|
|BSU10540||ntdB||biosynthesis of neotrehalosadiamine (3,3'-diamino-3,3'-dideoxy-alpha,beta-trehalose); hydrolase (RefSeq)||310, 311|
|BSU11110||yitS||hypothetical protein (RefSeq)||157, 215|
|BSU11270||yjzD||hypothetical protein (RefSeq)||64, 157|
|BSU11280||yjaU||hypothetical protein (RefSeq)||64, 157|
|BSU11890||yjcK||putative ribosomal-protein-alanine N-acetyltransferase (RefSeq)||157, 216|
|BSU11900||yjcL||putative integral inner membrane protein; possibly aquaporin-related (RefSeq)||52, 311|
|BSU12200||yjiA||hypothetical protein (RefSeq)||115, 157|
|BSU14080||ykuH||hypothetical protein (RefSeq)||151, 157|
|BSU14480||abh||transcriptional regulator (RefSeq)||39, 311|
|BSU17090||pksB||putative hydrolase (RefSeq)||222, 311|
|BSU18390||yoeC||putative bacteriophage integrase (RefSeq)||94, 157|
|BSU19020||yobN||putative amine oxidase (RefSeq)||114, 157|
|BSU19190||desK||two-component sensor histidine kinase [DesR] (RefSeq)||157, 406|
|BSU19200||desR||two-component response regulator [DesK] (RefSeq)||157, 378|
|BSU19350||yocS||putative sodium-dependent transporter (RefSeq)||157, 365|
|BSU21750||scuA||assembly factor BSco of the Cu(A) site of cytochrome c oxidase (RefSeq)||157, 219|
|BSU21840||ypjP||hypothetical protein (RefSeq)||39, 311|
|BSU21960||ypeQ||hypothetical protein (RefSeq)||244, 311|
|BSU21970||ypeP||hypothetical protein (RefSeq)||157, 311|
|BSU21980||ypdP||putative integral inner membrane protein (RefSeq)||157, 311|
|BSU21990||ypdQ||hypothetical protein (RefSeq)||39, 311|
|BSU22940||prsW||protease required for RsiW anti-sigma(W) degradation (RefSeq)||123, 311|
|BSU23000||ypbE||hypothetical protein (RefSeq)||151, 311|
|BSU23020||recQ||ATP-dependent DNA helicase (RefSeq)||151, 311|
|BSU23030||ypbB||hypothetical protein (RefSeq)||151, 311|
|BSU23320||ypzC||hypothetical protein (RefSeq)||121, 157|
|BSU26620||yrdR||putative efflux transporter (RefSeq)||157, 226|
|BSU26880||yraM||hypothetical protein (RefSeq)||39, 311|
|BSU27190||yrzI||hypothetical protein (RefSeq)||49, 157|
|BSU28620||rnhC||ribonuclease HIII (RefSeq)||200, 311|
|BSU29030||ytcD||putative transcriptional regulator (MarD family) (RefSeq)||157, 161|
|BSU36540||ywnJ||putative integral inner membrane protein (RefSeq)||157, 311|
|BSU37740||bacA||bacilysin biosynthesis protein, dehydratase (RefSeq)||157, 217|
|BSU38360||ywbD||putative AdoMet-dependent methyltransferase (RefSeq)||116, 157|
|BSU40840||yyaJ||putative transporter (RefSeq)||222, 311|
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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