Organism : Bacillus subtilis | Module List :
BSU09380 nsrR

NO-dependent activator of the ResDE regulon (RefSeq)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulator cog/ cog
rrf2_super tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU09380
(Mouseover regulator name to see its description)

BSU09380 is regulated by 21 influences and regulates 13 modules.
Regulators for BSU09380 nsrR (21)
Regulator Module Operator
BSU05970 222 tf
BSU06140 222 tf
BSU08730 222 tf
BSU09380 222 tf
BSU17590 222 tf
BSU17850 222 tf
BSU26220 222 tf
BSU30150 222 tf
BSU34200 222 tf
BSU05970 311 tf
BSU06540 311 tf
BSU08410 311 tf
BSU08520 311 tf
BSU09380 311 tf
BSU09480 311 tf
BSU09650 311 tf
BSU14480 311 tf
BSU17850 311 tf
BSU18760 311 tf
BSU19540 311 tf
BSU40800 311 tf
Regulated by BSU09380 (13)
Module Residual Genes
29 0.48 26
59 0.42 24
147 0.26 13
149 0.48 27
165 0.43 7
200 0.48 29
201 0.34 20
215 0.42 26
222 0.48 24
262 0.43 23
311 0.42 27
359 0.48 25
387 0.38 20
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5388 2.60e-01 ac.gGtcCgGAtAaaGgcatcggt
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5389 2.40e+02 AGGAGgta
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5560 5.30e-01 AAAGGagg
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5561 5.80e+02 TaCA.TCgcCTTtccattCaTta
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for BSU09380

BSU09380 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulator cog/ cog
rrf2_super tigr/ tigrfam
Module neighborhood information for BSU09380

BSU09380 has total of 48 gene neighbors in modules 222, 311
Gene neighbors (48)
Gene Common Name Description Module membership
BSU01820 adaB O6-methylguanine-DNA methyltransferase (RefSeq) 26, 222
BSU02030 ybdM putative protein kinase (RefSeq) 222, 291
BSU02340 gltP proton/glutamate symport protein (RefSeq) 26, 222
BSU02610 ycbR hypothetical protein (RefSeq) 222, 305
BSU06000 ydiK hypothetical protein (RefSeq) 39, 311
BSU06170 ydjE putative sugar kinase (ribokinase family) (RefSeq) 222, 231
BSU06800 yezA hypothetical protein (RefSeq) 129, 311
BSU06820 yeeG putative phage receptor protein (RefSeq) 39, 222
BSU07320 yfnC putative efflux transporter (RefSeq) 86, 311
BSU07530 yfmB hypothetical protein (RefSeq) 222, 359
BSU07540 yfmA hypothetical protein (RefSeq) 222, 359
BSU08720 ygaF putative bacterioferritin comigratory protein; putative peroxiredoxin (RefSeq) 222, 404
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
BSU09590 yhdT hypothetical protein (RefSeq) 26, 222
BSU09630 yhdX hypothetical protein (RefSeq) 39, 222
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
BSU11900 yjcL putative integral inner membrane protein; possibly aquaporin-related (RefSeq) 52, 311
BSU13190 ispA intracellular serine protease (RefSeq) 222, 231
BSU13630 ykvA hypothetical protein (RefSeq) 222, 389
BSU14020 ykyB hypothetical protein (RefSeq) 215, 222
BSU14480 abh transcriptional regulator (RefSeq) 39, 311
BSU17090 pksB putative hydrolase (RefSeq) 222, 311
BSU17480 ynzF hypothetical protein (RefSeq) 39, 222
BSU17560 ynaI hypothetical protein (RefSeq) 205, 222
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
BSU25940 yqcD conserved hypothetical protein; skin element (RefSeq) 86, 222
BSU26570 yrkB hypothetical protein (RefSeq) 86, 222
BSU26880 yraM hypothetical protein (RefSeq) 39, 311
BSU28620 rnhC ribonuclease HIII (RefSeq) 200, 311
BSU36540 ywnJ putative integral inner membrane protein (RefSeq) 157, 311
BSU38920 pepT peptidase T (RefSeq) 113, 222
BSU40270 yycP hypothetical protein (RefSeq) 26, 222
BSU40280 yycO hypothetical protein (RefSeq) 26, 222
BSU40840 yyaJ putative transporter (RefSeq) 222, 311
Gene Page Help

Network Tab

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.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

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.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

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.

Functions Tab

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.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

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.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our 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)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for BSU09380
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our 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)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend