Organism : Bacillus subtilis | Module List :
BSU29000 nrdR

transcriptional regulator NrdR (RefSeq)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains cog/ cog
TIGR00244 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU29000
(Mouseover regulator name to see its description)

BSU29000 is regulated by 26 influences and regulates 14 modules.
Regulators for BSU29000 nrdR (26)
Regulator Module Operator
BSU04770 270 tf
BSU05370 270 tf
BSU05850 270 tf
BSU08410 270 tf
BSU09480 270 tf
BSU10510 270 tf
BSU25100 270 tf
BSU26430 270 tf
BSU29000 270 tf
BSU33670 270 tf
BSU39990 270 tf
BSU40010 270 tf
BSU03880 94 tf
BSU05120 94 tf
BSU05390 94 tf
BSU05700 94 tf
BSU06580 94 tf
BSU13310 94 tf
BSU18420 94 tf
BSU21780 94 tf
BSU25100 94 tf
BSU27000 94 tf
BSU27120 94 tf
BSU29000 94 tf
BSU30020 94 tf
BSU33650 94 tf
Regulated by BSU29000 (14)
Module Residual Genes
92 0.45 27
94 0.49 29
144 0.35 21
158 0.38 22
161 0.43 26
173 0.56 16
185 0.25 17
215 0.42 26
247 0.42 29
270 0.52 28
292 0.47 22
301 0.45 18
341 0.54 16
397 0.33 21
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5142 7.30e+03 t.Aa.gGaGGa
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5143 1.20e+02 AatGtTtTaCAATtaATGTcAT
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5478 8.40e-01 cTgTgcaGaAcGcaggTcgtc
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5479 8.10e-01 AAAcCCcTggctcATtTTTttTGc
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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 BSU29000

BSU29000 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains cog/ cog
TIGR00244 tigr/ tigrfam
Module neighborhood information for BSU29000

BSU29000 has total of 55 gene neighbors in modules 94, 270
Gene neighbors (55)
Gene Common Name Description Module membership
BSU00440 veg hypothetical protein (RefSeq) 94, 115
BSU03140 tmrB ATP-binding tunicamycin resistance protein (RefSeq) 94, 115
BSU03150 aroK shikimate kinase (RefSeq) 94, 115
BSU03880 yczG putative transcriptional regulator (ArsR family) (RefSeq) 94, 115
BSU04320 ydaO putative metabolite transporter (RefSeq) 38, 270
BSU05390 ydfF putative transcriptional regulator (RefSeq) 94, 116
BSU05690 ydhB putative integral inner membrane protein (RefSeq) 270, 294
BSU05700 ydhC putative transcriptional regulator (GntR family) (RefSeq) 270, 323
BSU07400 yfmO metal efflux transporter (RefSeq) 161, 270
BSU07970 yfjT hypothetical protein (RefSeq) 94, 157
BSU08400 yfiU putative efflux transporter (RefSeq) 270, 327
BSU08520 recX recombination regulator RecX (RefSeq) 94, 258
BSU08530 yfhH hypothetical protein (RefSeq) 94, 270
BSU09610 yhdV integral membrane protein possibly involved in chromosome condensation (RefSeq) 94, 258
BSU10010 trpP tryptophan transporter (RefSeq) 64, 94
BSU12820 spoIISB two-component apoptotic control system component B (RefSeq) 94, 215
BSU12830 spoIISA two-component apoptosis factor (RefSeq) 94, 215
BSU13980 pbpH penicillin-binding enzyme for formation of rod-shaped peptidoglycan cell wall (RefSeq) 70, 94
BSU14840 ylaN hypothetical protein (RefSeq) 94, 310
BSU18110 ynfC hypothetical protein (RefSeq) 44, 94
BSU18390 yoeC putative bacteriophage integrase (RefSeq) 94, 157
BSU19300 yozC hypothetical protein (RefSeq) 94, 215
BSU21810 dfrA dihydrofolate reductase (RefSeq) 228, 270
BSU21820 thyA thymidylate synthase (RefSeq) 270, 301
BSU21910 metA homoserine O-succinyltransferase (RefSeq) 94, 327
BSU22980 ypbG putative phosphoesterase (RefSeq) 94, 258
BSU23040 fer ferredoxin (RefSeq) 94, 151
BSU23230 ypuF hypothetical protein (RefSeq) 94, 226
BSU23240 ypzK putative acetyltransferase (RefSeq) 94, 208
BSU23310 sipS type I signal peptidase (RefSeq) 94, 159
BSU23540 yqkK hypothetical protein (RefSeq) 129, 270
BSU23700 yqjX hypothetical protein (RefSeq) 161, 270
BSU23710 yqjW DNA polymerase IV (RefSeq) 161, 270
BSU23720 yqzH hypothetical protein (RefSeq) 159, 270
BSU23830 yqjL putative hydrolase (RefSeq) 94, 217
BSU26190 yqaT putative phage-related terminase large subunit; skin element (RefSeq) 238, 270
BSU26420 yrkQ two-component sensor histidine kinase [YrkP] (RefSeq) 129, 270
BSU26540 yrkE hypothetical protein (RefSeq) 71, 270
BSU26660 yrdN putative tautomerase (RefSeq) 129, 270
BSU26670 gltR transcriptional regulator (LysR family) (RefSeq) 38, 270
BSU26680 yrdK hypothetical protein (RefSeq) 89, 270
BSU26790 aadK aminoglycoside 6-adenylyltransferase (RefSeq) 94, 404
BSU26800 yrpB putative anionic nitroalkane dioxygenase (RefSeq) 35, 94
BSU26810 yrpC glutamate racemase (RefSeq) 270, 310
BSU27140 oatA peptidoglycan O-acetyltransferase (RefSeq) 38, 270
BSU28180 ysxD putative integral inner membrane protein (RefSeq) 151, 270
BSU29000 nrdR transcriptional regulator NrdR (RefSeq) 94, 270
BSU32140 paiB putative enzyme (RefSeq) 241, 270
BSU38450 ywaE putative transcriptional regulator (MarR family) (RefSeq) 94, 341
BSU38480 ywaC (p)ppGpp synthetase (RefSeq) 71, 94
BSU39990 yxaF transcriptional regulator (RefSeq) 38, 270
BSU40010 yxaD putative transcriptional regulator (MarR family) (RefSeq) 161, 270
BSU40710 yybA putative transcriptional regulator (MarR family) (RefSeq) 270, 310
BSU40720 yyaT putative acetyltransferase (RefSeq) 151, 270
BSU40730 yyaS putative integral inner membrane protein (RefSeq) 151, 270
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 BSU29000
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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