Organism : Bacillus subtilis | Module List :
BSU40130 yydK

putative transcriptional regulator (GntR family) (RefSeq)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU40130
(Mouseover regulator name to see its description)

BSU40130 is regulated by 30 influences and regulates 2 modules.
Regulators for BSU40130 yydK (30)
Regulator Module Operator
BSU01810 171 tf
BSU02220 171 tf
BSU08250 171 tf
BSU09330 171 tf
BSU09990 171 tf
BSU10860 171 tf
BSU12370 171 tf
BSU16600 171 tf
BSU19120 171 tf
BSU24250 171 tf
BSU24320 171 tf
BSU34180 171 tf
BSU34200 171 tf
BSU40130 171 tf
BSU01430 318 tf
BSU02550 318 tf
BSU03560 318 tf
BSU05370 318 tf
BSU07010 318 tf
BSU07590 318 tf
BSU08370 318 tf
BSU10880 318 tf
BSU23090 318 tf
BSU26320 318 tf
BSU33580 318 tf
BSU34060 318 tf
BSU34180 318 tf
BSU34630 318 tf
BSU39430 318 tf
BSU40130 318 tf

Warning: BSU40130 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
5290 1.60e-04 gaAGgGGg
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5291 6.20e+02 aaaagaaaGGa
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5574 2.90e-03 aaGgggGg
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5575 1.50e+03 CGgagTGAGAA
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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 BSU40130

BSU40130 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU40130

BSU40130 has total of 56 gene neighbors in modules 171, 318
Gene neighbors (56)
Gene Common Name Description Module membership
BSU01710 ybbJ putative acyltransferase (RefSeq) 171, 350
BSU01720 ybbK hypothetical protein (RefSeq) 171, 350
BSU02090 ybxI exported beta-lactamase (RefSeq) 171, 287
BSU02440 glnJ two-component sensor histidine kinase [GlnL] for glutamine degradation (RefSeq) 318, 361
BSU03560 ycxD putative PLP-dependent transcriptional regulator (RefSeq) 71, 318
BSU05220 ydeJ putative lipoprotein (RefSeq) 171, 287
BSU07440 yfmK putative acetyltransferase (RefSeq) 171, 287
BSU08250 yfiF putative transcriptional regulator (AraC/XylS family; cupin family) (RefSeq) 114, 171
BSU08380 yfiS putative efflux transporter (RefSeq) 152, 318
BSU09320 yhcY two-component sensor histidine kinase [YhcZ] (RefSeq) 114, 318
BSU09330 yhcZ two-component response regulator [YhcY] (RefSeq) 114, 318
BSU09490 yhdJ putative acetyltransferase (RefSeq) 145, 318
BSU09760 yheE hypothetical protein (RefSeq) 115, 171
BSU10860 yisT hypothetical protein (RefSeq) 101, 171
BSU10880 yisV putative PLP-dependent transcriptional regulator (RefSeq) 64, 318
BSU10990 yitH putative N-acetyltransferase (RefSeq) 64, 171
BSU12380 uxaB altronate oxidoreductase (RefSeq) 71, 318
BSU12390 uxaA altronate hydrolase (RefSeq) 180, 318
BSU13070 ykkA hypothetical protein (RefSeq) 64, 171
BSU13080 ykkB putative N-acetyltransferase (RefSeq) 64, 171
BSU13940 ykwB putative acetyltransferase (RefSeq) 171, 287
BSU18370 yoeA putative efflux transporter (RefSeq) 171, 287
BSU24780 yqgY hypothetical protein (RefSeq) 70, 171
BSU26180 yqbA putative phage capsid protein; skin element (RefSeq) 318, 387
BSU26370 yqaC hypothetical protein (RefSeq) 171, 287
BSU28420 ysmA hypothetical protein (RefSeq) 171, 287
BSU30360 yttA hypothetical protein (RefSeq) 171, 287
BSU30390 bceS two-component sensor histidine kinase controlling resistance to antibiotics affecting the envelope [YtsA] (RefSeq) 71, 171
BSU30400 bceR two-component response regulator controlling resistance to antibiotics affecting the envelope [YtsB] (RefSeq) 71, 171
BSU32080 yuiB hypothetical protein (RefSeq) 101, 171
BSU32090 yuiA hypothetical protein (RefSeq) 101, 171
BSU32210 yuzD putative sulfur oxido-reduction management enzyme (RefSeq) 71, 171
BSU32440 pucK uric acid permease (RefSeq) 84, 318
BSU32520 pucG putative ureidoglycolate lyase (ureidoglycolase) (RefSeq) 219, 318
BSU32530 yurH allantoate amidohydrolase (RefSeq) 89, 318
BSU33560 yvaD putative integral inner membrane protein (RefSeq) 111, 318
BSU33570 yvaE putative metabolite-efflux transporter (RefSeq) 111, 318
BSU33580 yvaF putative transcriptional regulator (RefSeq) 111, 318
BSU34060 yvfU two-component response regulator [YvfT] (RefSeq) 318, 361
BSU34070 yvfT two-component sensor histidine kinase [YvfU] (RefSeq) 318, 361
BSU34080 yvfS putative ABC transporter (permease) (RefSeq) 318, 326
BSU34090 yvfR putative ABC efflux transporter (ATP-binding protein) (RefSeq) 318, 326
BSU34200 sigL RNA polymerase sigma-54 factor (sigma-L) (RefSeq) 171, 208
BSU34630 mdxR putative transcriptional regulator (LacI family) (RefSeq) 90, 318
BSU35880 pgsA capsular polyglutamate synthetase (RefSeq) 64, 318
BSU36320 ywpG hypothetical protein (RefSeq) 64, 318
BSU36340 ywpE putative sortase (RefSeq) 291, 318
BSU38640 yxlH putative efflux transporter (RefSeq) 180, 318
BSU39860 aldX putative aldehyde dehydrogenase (RefSeq) 156, 318
BSU40110 bglA aryl-6-phospho-beta-glucosidase (RefSeq) 61, 318
BSU40120 yyzE putative phosphotransferase system enzyme IIA component (RefSeq) 248, 318
BSU40130 yydK putative transcriptional regulator (GntR family) (RefSeq) 171, 318
BSU40260 yycQ putative conserved membrane protein (RefSeq) 248, 318
BSU40310 phrG secreted regulator of the activity of phosphatase RapG (RefSeq) 101, 171
BSU40640 yybH hypothetical protein (RefSeq) 171, 287
BSU40700 yybB putative hydrolase (RefSeq) 318, 378
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 BSU40130
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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