Organism : Bacillus subtilis | Module List :
BSU04460 dctR

two-component response regulator (RefSeq)

CircVis
Functional Annotations (8)
Function System
Response regulator of citrate/malate metabolism cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
pilus go/ cellular_component
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU04460
(Mouseover regulator name to see its description)

BSU04460 is regulated by 17 influences and regulates 11 modules.
Regulators for BSU04460 dctR (17)
Regulator Module Operator
BSU02550 361 tf
BSU04100 361 tf
BSU04460 361 tf
BSU06860 361 tf
BSU10560 361 tf
BSU11660 361 tf
BSU14740 361 tf
BSU29740 361 tf
BSU33080 361 tf
BSU34060 361 tf
BSU37580 361 tf
BSU39990 361 tf
BSU04460 246 tf
BSU07820 246 tf
BSU09480 246 tf
BSU27120 246 tf
BSU33950 246 tf

Warning: BSU04460 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
5434 3.80e-05 TtaTacttaAaaagggGgAt
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5435 4.20e-03 Aa.gAC.ttAaagGAgAAGcT
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5646 2.40e-08 tttgtAtaAgggGGGaaA.gAc
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5647 3.10e-03 AAaggagaaggtgataaAaAgAaa
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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 BSU04460

BSU04460 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Response regulator of citrate/malate metabolism cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
pilus go/ cellular_component
Two-component system kegg/ kegg pathway
Module neighborhood information for BSU04460

BSU04460 has total of 49 gene neighbors in modules 246, 361
Gene neighbors (49)
Gene Common Name Description Module membership
BSU00400 yabE putative cell wall shaping enzyme (RefSeq) 53, 246
BSU02440 glnJ two-component sensor histidine kinase [GlnL] for glutamine degradation (RefSeq) 318, 361
BSU02730 natK two-component sensor histidine kinase [NatR] (RefSeq) 130, 246
BSU02740 natR two-component response regulator [NatK] (RefSeq) 130, 246
BSU02750 natA Na+ ABC efflux transporter (ATP-binding protein) (RefSeq) 130, 246
BSU02760 natB Na+ ABC efflux transporter (permease) (RefSeq) 130, 246
BSU04440 dctB C4-dicarboxylate binding protein (RefSeq) 246, 361
BSU04450 dctS two-component sensor histidine kinase (RefSeq) 246, 361
BSU04460 dctR two-component response regulator (RefSeq) 246, 361
BSU06860 yezE putative transcriptional regulator (TetR family) (RefSeq) 233, 361
BSU06870 yesE hypothetical protein (RefSeq) 307, 361
BSU06880 yesF hypothetical protein (RefSeq) 10, 361
BSU08040 yfjM hypothetical protein (RefSeq) 102, 361
BSU08120 yfjF hypothetical protein (RefSeq) 55, 246
BSU09150 yhcN putative lipoprotein (RefSeq) 43, 246
BSU10640 sbcD DNA repair exonuclease (RefSeq) 50, 361
BSU10650 sbcC DNA ATP-dependent repair enzyme (RefSeq) 50, 361
BSU10660 yisB putative nuclease component (RefSeq) 50, 361
BSU12490 yjqC putative PBSX phage manganese-containing catalase (RefSeq) 231, 246
BSU14710 ylaA hypothetical protein (RefSeq) 89, 361
BSU14740 ylaD anti-YlaC sigma factor (RefSeq) 231, 361
BSU17070 ymcC putative integral inner membrane protein (RefSeq) 246, 285
BSU17640 alrB alanine racemase (RefSeq) 246, 301
BSU18860 yozH hypothetical protein (RefSeq) 246, 411
BSU22920 ypeB spore membrane component (RefSeq) 246, 357
BSU22930 sleB spore cortex-lytic enzyme (RefSeq) 246, 357
BSU23390 spoVAF stage V sporulation protein AF (RefSeq) 246, 357
BSU24230 spoIVB regulatory membrane-associated serine protease (RefSeq) 246, 357
BSU25080 yqfX hypothetical protein (RefSeq) 43, 246
BSU32720 yurZ hypothetical protein (RefSeq) 246, 301
BSU34010 yvbW putative amino acid permease (RefSeq) 322, 361
BSU34060 yvfU two-component response regulator [YvfT] (RefSeq) 318, 361
BSU34070 yvfT two-component sensor histidine kinase [YvfU] (RefSeq) 318, 361
BSU34960 yvoF putative O-acetyltransferase (RefSeq) 106, 361
BSU34970 hprP pyrophosphatase PpaX (RefSeq) 106, 361
BSU34980 yvoD putative integral inner membrane protein (RefSeq) 106, 361
BSU34990 lgt prolipoprotein diacylglyceryl transferase (RefSeq) 106, 361
BSU35000 hprK HPr kinase/phosphorylase (RefSeq) 106, 361
BSU35010 nagA N-acetylglucosamine-6-phosphate deacetylase (RefSeq) 334, 361
BSU35020 nagBA N-acetylglucosamine-6-phosphate isomerase (RefSeq) 334, 361
BSU36100 ywrD putative gamma-glutamyltransferase (RefSeq) 241, 246
BSU37190 clsB cardiolipin synthetase (RefSeq) 22, 246
BSU38420 sacY transcriptional antiterminator (RefSeq) 241, 246
BSU39029 yxiT 150, 246
BSU39650 yxdK two-component sensor histidine kinase [YxdJ] (RefSeq) 89, 361
BSU39660 yxdJ two-component response regulator [YxdK] (RefSeq) 89, 361
BSU40320 argI arginase (RefSeq) 229, 246
BSU40330 rocE arginine/ornithine/gamma-aminobutyrate permease (RefSeq) 229, 246
VIMSS37672 VIMSS37672 None 184, 361
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 BSU04460
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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