Organism : Bacillus subtilis | Module List :
BSU33080 liaR

two-component response regulator [YvqE] responding to cell wall stress (RefSeq)

CircVis
Functional Annotations (8)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain 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
sequence-specific DNA binding go/ molecular_function
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU33080
(Mouseover regulator name to see its description)

BSU33080 is regulated by 28 influences and regulates 16 modules.
Regulators for BSU33080 liaR (28)
Regulator Module Operator
BSU01010 319 tf
BSU01810 319 tf
BSU02680 319 tf
BSU03080 319 tf
BSU03850 319 tf
BSU04650 319 tf
BSU05330 319 tf
BSU08300 319 tf
BSU13210 319 tf
BSU15470 319 tf
BSU15970 319 tf
BSU19070 319 tf
BSU33080 319 tf
BSU34170 319 tf
BSU36300 319 tf
BSU38600 319 tf
BSU01010 48 tf
BSU08300 48 tf
BSU15970 48 tf
BSU23210 48 tf
BSU24250 48 tf
BSU29740 48 tf
BSU30020 48 tf
BSU30460 48 tf
BSU33080 48 tf
BSU33990 48 tf
BSU35050 48 tf
BSU39990 48 tf

Warning: BSU33080 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
5054 2.10e+03 AAagaGCCGGg
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5055 5.00e+01 ataAaAAAAGc
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5576 1.70e+00 ctTTttTaTcg
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5577 7.10e+01 GCCgctTC
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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 BSU33080

BSU33080 is enriched for 8 functions in 3 categories.
Module neighborhood information for BSU33080

BSU33080 has total of 45 gene neighbors in modules 48, 319
Gene neighbors (45)
Gene Common Name Description Module membership
BSU00410 rnmV ribonuclease M5 (RefSeq) 48, 397
BSU00420 ksgA dimethyladenosine transferase (RefSeq) 48, 397
BSU01580 ybaR putative permease (RefSeq) 48, 397
BSU03580 yczE integral inner membrane protein regulating antibiotic production (RefSeq) 132, 319
BSU05930 rimI ribosomal protein S18 alanine N-acetyltransferase (RefSeq) 1, 48
BSU07340 yfnA metabolite permease (RefSeq) 190, 319
BSU08030 dusC tRNA-dihydrouridine synthase 2 (RefSeq) 319, 397
BSU08300 yfiK two-component response regulator [YfiJ] (RefSeq) 48, 307
BSU08930 cspR putative rRNA methylase (RefSeq) 197, 319
BSU13730 queD 6-pyruvoyl tetrahydrobiopterin synthase-like; queuosine biosynthesis (RefSeq) 319, 409
BSU13740 queE queuosine biosynthesis enzyme (RefSeq) 319, 409
BSU16920 pgsA CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase (RefSeq) 48, 245
BSU16930 cinA competence damage-inducible protein A (RefSeq) 48, 245
BSU19440 yojI multidrug efflux protein (RefSeq) 319, 397
BSU19650 yodM putative phospholipid phosphatase (RefSeq) 48, 319
BSU22150 ypvA putative ATP-dependent helicase (RefSeq) 271, 319
BSU23950 yqjA hypothetical protein (RefSeq) 67, 319
BSU24830 yqgT putative gamma-D-glutamyl-L-diamino acid endopeptidase (RefSeq) 37, 319
BSU25670 yqeH GTP-binding protein YqeH (RefSeq) 48, 314
BSU25680 yqeG putative hydrolase (RefSeq) 48, 314
BSU29600 braB branched-chain amino acid-Na+ symporter (RefSeq) 13, 319
BSU29720 ytxE flagellar motor protein MotS (RefSeq) 48, 202
BSU29730 ytxD flagellar motor protein MotP (RefSeq) 48, 190
BSU30490 ytqB putative RNA methylase (RefSeq) 271, 319
BSU30820 menD 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate synthase (RefSeq) 132, 319
BSU30990 thiT thiamin permease (RefSeq) 13, 319
BSU31090 ktrA potassium uptake protein (RefSeq) 48, 397
BSU32040 yuiF amino acid transporter (RefSeq) 72, 319
BSU33080 liaR two-component response regulator [YvqE] responding to cell wall stress (RefSeq) 48, 319
BSU33090 liaS two-component sensor histidine kinase [YvqC] sensing cell wall stress (RefSeq) 48, 319
BSU33100 liaF integral inner membrane protein (RefSeq) 66, 319
BSU33150 yvqK ATP:cob(I)alamin adenosyltransferase (RefSeq) 1, 48
BSU33160 yvrA putative vitamin B12 transport system, ATPase component (RefSeq) 48, 190
BSU33170 yvrB putative vitamin B12 permease (RefSeq) 1, 48
BSU33180 yvrC putative lipoprotein binding vitamin B12 (RefSeq) 48, 63
BSU33330 lysP lysine permease (RefSeq) 319, 339
BSU33350 yvsG putative membrane hydrolase (RefSeq) 11, 319
BSU34100 rsbQ regulator of RsbP phosphatase (RefSeq) 132, 319
BSU36290 ywpJ putative phosphatase (RefSeq) 319, 327
BSU36300 glcR transcriptional regulator (DeoR family) (RefSeq) 319, 327
BSU36610 ywnC putative integral inner membrane protein (RefSeq) 132, 319
BSU37150 pyrG CTP synthetase (RefSeq) 190, 319
BSU37490 speB agmatinase (RefSeq) 48, 190
BSU37590 ywgA hypothetical protein (RefSeq) 48, 322
BSU37600 ywfO putative metal-dependent phosphohydrolase (RefSeq) 48, 322
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 BSU33080
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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