Organism : Bacillus subtilis | Module List :
BSU02000 ybdJ

two-component response regulator [YbdK] (RefSeq)

CircVis
Functional Annotations (5)
Function System
Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU02000
(Mouseover regulator name to see its description)

BSU02000 is regulated by 19 influences and regulates 21 modules.
Regulators for BSU02000 ybdJ (19)
Regulator Module Operator
BSU02000 312 tf
BSU02160 312 tf
BSU06700 312 tf
BSU07820 312 tf
BSU08730 312 tf
BSU10560 312 tf
BSU16900 312 tf
BSU24220 312 tf
BSU26220 312 tf
BSU35030 312 tf
BSU02000 360 tf
BSU02320 360 tf
BSU03890 360 tf
BSU06960 360 tf
BSU07820 360 tf
BSU08100 360 tf
BSU26320 360 tf
BSU30150 360 tf
BSU37290 360 tf
Regulated by BSU02000 (21)
Module Residual Genes
10 0.37 22
20 0.33 22
21 0.33 19
39 0.42 28
130 0.44 28
143 0.31 18
168 0.50 25
201 0.34 20
206 0.40 21
244 0.32 22
277 0.31 18
281 0.36 25
285 0.44 25
294 0.35 20
297 0.36 22
305 0.41 23
312 0.30 23
326 0.42 24
358 0.36 21
360 0.35 21
371 0.37 22
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5562 5.10e-01 gaaAGGAG
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5563 9.20e+03 CTGgctcgAagCG
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5644 4.50e-02 GTaAGCgcTttCt.taaagg
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5645 5.70e+01 GGggaaAttCA
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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 BSU02000

BSU02000 is enriched for 5 functions in 3 categories.
Module neighborhood information for BSU02000

BSU02000 has total of 43 gene neighbors in modules 312, 360
Gene neighbors (43)
Gene Common Name Description Module membership
BSU01990 ybdG putative hydrolase/transferase (RefSeq) 89, 360
BSU02000 ybdJ two-component response regulator [YbdK] (RefSeq) 312, 360
BSU02320 ybfP putative transcriptional regulator (AraC/XylS family) (RefSeq) 8, 360
BSU02540 ycbK putative efflux transporter (RefSeq) 312, 372
BSU02570 ycbN putative ABC efflux transporter (ATP-binding protein) (RefSeq) 135, 312
BSU03890 gabR transcriptional regulator (GntR/MocR family) with PLP binding site (RefSeq) 175, 360
BSU05720 ydhE putative glycosyltransferase (RefSeq) 285, 360
BSU05910 ydiB putative ATPase or kinase UPF0079 (RefSeq) 75, 312
BSU05920 ydiC putative chaperone or protease (RefSeq) 135, 312
BSU06210 ydjI hypothetical protein (RefSeq) 162, 312
BSU06670 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C (RefSeq) 312, 382
BSU06680 gatA aspartyl/glutamyl-tRNA amidotransferase subunit A (RefSeq) 312, 382
BSU06970 yesO pectin degradation byproducts-binding lipoprotein (RefSeq) 143, 360
BSU06980 yesP rhamnogalacturonan permease (RefSeq) 143, 360
BSU06990 yesQ rhamnogalacturonan permease (RefSeq) 360, 371
BSU07000 yesR rhamnogalacturonan hydrolase (RefSeq) 10, 360
BSU07020 rhgT rhamnogalacturonan acetylesterase (RefSeq) 143, 360
BSU07040 yesV putative integral inner membrane component (RefSeq) 10, 360
BSU07050 yesW polysaccharide lyase; lipoprotein (RefSeq) 360, 372
BSU07060 yesX polysaccharide lyase (RefSeq) 360, 372
BSU07090 yetA putative enzyme (RefSeq) 143, 360
BSU07110 lplB putative ABC transporter (permease) (RefSeq) 360, 372
BSU07120 lplC putative ABC transporter (permease) (RefSeq) 143, 360
BSU07160 yetH putative lyase/dioxygenase (RefSeq) 83, 312
BSU07630 nosA nitric-oxide synthase (RefSeq) 135, 312
BSU08280 yfiI putative oxidoreductase (RefSeq) 360, 371
BSU09800 yheA hypothetical protein (RefSeq) 135, 312
BSU10810 yisP putative squalene/phytoene synthase (RefSeq) 135, 312
BSU17430 ynbA putative GTP-binding protein protease modulator (RefSeq) 135, 312
BSU17440 ynbB putative C-S lyase (RefSeq) 135, 312
BSU17650 yncE putative prophage protein (RefSeq) 135, 312
BSU18090 parE DNA topoisomerase IV subunit B (RefSeq) 135, 312
BSU18100 parC DNA topoisomerase IV subunit A (RefSeq) 135, 312
BSU22450 cca tRNA CCA-pyrophosphorylase (RefSeq) 312, 382
BSU22480 mgsA methylglyoxal synthase (RefSeq) 312, 382
BSU22490 dapB dihydrodipicolinate reductase (RefSeq) 312, 382
BSU22500 ypjD nucleotide phosphohydrolase (RefSeq) 312, 382
BSU28670 ysfB putative regulator (RefSeq) 285, 312
BSU30100 yteT putative dehydrogenase of rhamnogalaturonan degradation (RefSeq) 360, 371
BSU30110 yteS putative lipoprotein required for rhamnogalaturonan degradation (RefSeq) 360, 371
BSU30120 yteR unsaturated rhamnogalacturonyl hydrolase (RefSeq) 360, 371
BSU34190 yvfH putative lactate permease (RefSeq) 330, 360
BSU36510 amtB ammonium transporter (RefSeq) 10, 312
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 BSU02000
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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