Organism : Bacillus subtilis | Module List :
BSU29110 phoP

two-component response regulator (RefSeq)

CircVis
Functional Annotations (6)
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
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU29110
(Mouseover regulator name to see its description)

BSU29110 is regulated by 23 influences and regulates 9 modules.
Regulators for BSU29110 phoP (23)
Regulator Module Operator
BSU03080 131 tf
BSU03850 131 tf
BSU08190 131 tf
BSU15320 131 tf
BSU15330 131 tf
BSU28550 131 tf
BSU29110 131 tf
BSU29630 131 tf
BSU35910 131 tf
BSU36630 131 tf
BSU04160 22 tf
BSU04250 22 tf
BSU06960 22 tf
BSU09270 22 tf
BSU12000 22 tf
BSU14140 22 tf
BSU14380 22 tf
BSU27110 22 tf
BSU28550 22 tf
BSU29110 22 tf
BSU34480 22 tf
BSU35910 22 tf
BSU37310 22 tf

Warning: BSU29110 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
5006 3.20e+01 GtCAtaTgCcCcCCCgGAttGTTT
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5007 1.40e+02 TGtAaaCgctTtcttttatt
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5214 6.60e-01 AAAAGGgGgg
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5215 5.90e+02 GgGGaAgg
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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 BSU29110

BSU29110 is enriched for 6 functions in 3 categories.
Module neighborhood information for BSU29110

BSU29110 has total of 45 gene neighbors in modules 22, 131
Gene neighbors (45)
Gene Common Name Description Module membership
BSU00640 spoIIE serine phosphatase (RefSeq) 131, 141
BSU00650 yabS hypothetical protein (RefSeq) 131, 141
BSU04160 mtlR transcriptional regulator (RefSeq) 22, 61
BSU04240 ydzA hypothetical protein (RefSeq) 22, 189
BSU04250 lrpC transcriptional regulator (Lrp/AsnC family) (RefSeq) 22, 213
BSU06560 yerA putative amidohydrolase (RefSeq) 131, 189
BSU07610 citM transporter of divalent metal ions/citrate complexes (RefSeq) 131, 133
BSU07620 yflN putative metal-dependent hydrolase (RefSeq) 131, 133
BSU08740 ygzB hypothetical protein (RefSeq) 22, 404
BSU09280 glpF glycerol permease (RefSeq) 22, 330
BSU09290 glpK glycerol kinase (RefSeq) 22, 330
BSU09300 glpD glycerol-3-phosphate oxidase (RefSeq) 22, 411
BSU09680 nhaC Na+/H+ antiporter (RefSeq) 22, 241
BSU12000 manR transcriptional antiterminator (RefSeq) 22, 61
BSU12020 manA mannose-6 phosphate isomerase ; cupin family (RefSeq) 22, 61
BSU14060 ykuF short chain dehydrogenase (RefSeq) 131, 384
BSU14130 ykuL hypothetical protein (RefSeq) 22, 264
BSU14380 fruR transcriptional regulator (DeoR family) (RefSeq) 22, 164
BSU14390 fruK fructose-1-phosphate kinase (RefSeq) 22, 164
BSU15330 sigG sporulation sigma factor SigG (RefSeq) 131, 141
BSU17010 ymcB (dimethylallyl)adenosine tRNA methylthiotransferase (RefSeq) 22, 164
BSU19640 yodL hypothetical protein (RefSeq) 131, 208
BSU25190 cccA cytochrome c550 (RefSeq) 131, 210
BSU25290 era GTP-binding protein Era (RefSeq) 22, 97
BSU25300 cdd cytidine/deoxycytidine deaminase (RefSeq) 22, 97
BSU28520 etfA electron transfer flavoprotein (alpha subunit) (RefSeq) 131, 384
BSU28530 etfB electron transfer flavoprotein (beta subunit) (RefSeq) 131, 384
BSU28540 ysiB enoyl-CoA hydratase (RefSeq) 131, 384
BSU28550 fadR transcriptional regulator of fatty acids degradation (TetR/AcrR family) (RefSeq) 131, 384
BSU28810 abnA arabinan-endo 1,5-alpha-L-arabinase (RefSeq) 22, 329
BSU29010 speD S-adenosylmethionine decarboxylase proenzyme (RefSeq) 22, 241
BSU29100 phoR two-component sensor histidine kinase (RefSeq) 22, 131
BSU29110 phoP two-component response regulator (RefSeq) 22, 131
BSU30260 msmR transcriptional regulator (LacI family) (RefSeq) 22, 250
BSU30660 ytkA putative lipoprotein (RefSeq) 22, 340
BSU32820 fadE acyl-CoA dehydrogenase (FAD dependent) (RefSeq) 131, 384
BSU32830 yusK acetyl-CoA acetyltransferase (RefSeq) 131, 384
BSU32840 fadN enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase (RefSeq) 131, 384
BSU37170 acdA acyl-CoA dehydrogenase (RefSeq) 131, 384
BSU37180 fadF putative iron-sulphur-binding reductase (RefSeq) 131, 384
BSU37190 clsB cardiolipin synthetase (RefSeq) 22, 246
BSU37310 fnr transcriptional regulator (FNR/CAP family) (RefSeq) 22, 189
BSU39340 hutP anti-terminator HutP (RefSeq) 22, 330
BSU39400 pdp pyrimidine-nucleoside phosphorylase (RefSeq) 22, 164
BSU39430 deoR transcriptional regulator (RefSeq) 22, 340
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 BSU29110
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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