Organism : Bacillus subtilis | Module List :
BSU26430 yrkP

two-component response regulator [YrkQ] (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 BSU26430
(Mouseover regulator name to see its description)

BSU26430 is regulated by 24 influences and regulates 14 modules.
Regulators for BSU26430 yrkP (24)
Regulator Module Operator
BSU02160 44 tf
BSU05850 44 tf
BSU09500 44 tf
BSU15690 44 tf
BSU18740 44 tf
BSU19100 44 tf
BSU26220 44 tf
BSU26320 44 tf
BSU26430 44 tf
BSU26840 44 tf
BSU36600 44 tf
BSU40010 44 tf
BSU40800 44 tf
BSU00800 129 tf
BSU05060 129 tf
BSU05850 129 tf
BSU09480 129 tf
BSU09830 129 tf
BSU13870 129 tf
BSU18760 129 tf
BSU26320 129 tf
BSU26340 129 tf
BSU26430 129 tf
BSU33230 129 tf

Warning: BSU26430 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5048 4.90e+00 AtGcTC.CCACaAAT
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5049 2.10e+02 aaatccCtCcttT.taatt..t.t
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5210 8.80e+02 gtgatAaaAatGgaGagt.aa
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5211 5.90e+04 GGGGCAAaGG
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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 BSU26430

BSU26430 is enriched for 5 functions in 3 categories.
Module neighborhood information for BSU26430

BSU26430 has total of 53 gene neighbors in modules 44, 129
Gene neighbors (53)
Gene Common Name Description Module membership
BSU01520 ybaK putative alkylated deoxynucleotide triphosphohydrolase (RefSeq) 129, 174
BSU03680 yclG putative uronase (RefSeq) 129, 156
BSU04170 ydaB putative acyl-CoA ligase (RefSeq) 129, 387
BSU04290 ydaL hypothetical protein (RefSeq) 44, 213
BSU04310 ydaN putative regulator (RefSeq) 44, 213
BSU05040 yddN putative alkanal monooxygenase (RefSeq) 44, 95
BSU06790 yeeD hypothetical protein (RefSeq) 129, 178
BSU06800 yezA hypothetical protein (RefSeq) 129, 311
BSU07130 lplD putative glycosidase (RefSeq) 33, 129
BSU07140 yetF hypothetical protein (RefSeq) 129, 304
BSU07660 yflJ hypothetical protein (RefSeq) 123, 129
BSU09500 yhdK negative regulator of the activity of sigma-M (RefSeq) 38, 44
BSU13770 ykvO putative oxidoreductase (RefSeq) 44, 216
BSU13790 ykvQ putative sporulation-specific glycosylase (RefSeq) 44, 291
BSU14460 ykpC hypothetical protein (RefSeq) 129, 286
BSU17260 aprX alkaline serine protease (RefSeq) 129, 178
BSU17300 ebrA small multidrug resistance efflux transporter (RefSeq) 38, 44
BSU17410 cwlC N-acetylmuramoyl-L-alanine amidase (RefSeq) 44, 283
BSU17670 cotU spore coat protein (RefSeq) 44, 200
BSU17770 yndF putative spore germination lipoprotein (RefSeq) 44, 301
BSU18110 ynfC hypothetical protein (RefSeq) 44, 94
BSU18180 yngB putative UTP-sugar-phosphate uridylyltransferase (RefSeq) 44, 52
BSU18690 yoaP hypothetical protein (RefSeq) 64, 129
BSU18700 yoaQ hypothetical protein (RefSeq) 129, 411
BSU18740 yozG putative transcriptional regulator (RefSeq) 44, 47
BSU18960 yozM putative bacteriophage protein (RefSeq) 129, 181
BSU19800 phy phytase (RefSeq) 129, 231
BSU20710 yopZ conserved hypothetical protein; phage SPbeta (RefSeq) 44, 52
BSU23540 yqkK hypothetical protein (RefSeq) 129, 270
BSU24200 yqiH putative lipoprotein (RefSeq) 44, 52
BSU25900 cwlA N-acetylmuramoyl-L-alanine amidase; skin element (RefSeq) 44, 206
BSU25910 yqxH putative holin; skin element (RefSeq) 44, 206
BSU26060 yqbM hypothetical protein (RefSeq) 129, 130
BSU26130 yqbF hypothetical protein; skin element (RefSeq) 129, 238
BSU26150 yqbD putative DNA wielding protein; skin element (RefSeq) 129, 206
BSU26360 yqaD conserved hypothetical protein; skin element (RefSeq) 52, 129
BSU26410 yrkR phosphate-starvation-inducible protein PsiE (RefSeq) 44, 129
BSU26420 yrkQ two-component sensor histidine kinase [YrkP] (RefSeq) 129, 270
BSU26430 yrkP two-component response regulator [YrkQ] (RefSeq) 44, 129
BSU26440 yrkO putative integral inner membrane protein (RefSeq) 44, 129
BSU26490 yrkJ putative integral inner membrane protein (RefSeq) 44, 71
BSU26500 yrkI hypothetical protein (RefSeq) 44, 71
BSU26510 yrkH putative hydrolase (RefSeq) 44, 71
BSU26530 yrkF putative rhodanese-related sulfur transferase (RefSeq) 44, 71
BSU26600 bltD spermine/spermidine acetyltransferase (RefSeq) 115, 129
BSU26660 yrdN putative tautomerase (RefSeq) 129, 270
BSU26840 sigZ RNA polymerase sigma factor SigZ (RefSeq) 44, 206
BSU27150 yrhK hypothetical protein (RefSeq) 44, 387
BSU35040 yvnB putative exported phosphohydrolase (RefSeq) 44, 238
BSU35870 pgsE factor required for polyglutamate synthesis (RefSeq) 44, 61
BSU37040 ywkB putative transporter (RefSeq) 129, 387
BSU38390 ywbA putative phosphotransferase system enzyme IIC permease component (RefSeq) 44, 130
BSU40240 yycS putative integrase/transposase (RefSeq) 44, 285
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 BSU26430
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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