Organism : Bacillus subtilis | Module List :
BSU07820 treR

transcriptional regulator (GntR family) (RefSeq)

CircVis
Functional Annotations (5)
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
trehalos_R_Bsub tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU07820
(Mouseover regulator name to see its description)

BSU07820 is regulated by 17 influences and regulates 13 modules.
Regulators for BSU07820 treR (17)
Regulator Module Operator
BSU08100 321 tf
BSU19030 321 tf
BSU29700 321 tf
BSU35910 321 tf
BSU02000 10 tf
BSU02070 10 tf
BSU02160 10 tf
BSU02320 10 tf
BSU03890 10 tf
BSU05970 10 tf
BSU07010 10 tf
BSU07820 10 tf
BSU08100 10 tf
BSU17590 10 tf
BSU26220 10 tf
BSU26320 10 tf
BSU36600 10 tf

Warning: BSU07820 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
4982 1.60e+01 ATGaaAgCacTttaa
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4983 2.70e+01 GgagGaaT
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5580 3.70e-09 TtttAaAGCGcTTTCAacaTaGT
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5581 3.00e-04 CccgTaTatacAggtaGTcAacac
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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 BSU07820

BSU07820 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
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
trehalos_R_Bsub tigr/ tigrfam
Module neighborhood information for BSU07820

BSU07820 has total of 39 gene neighbors in modules 10, 321
Gene neighbors (39)
Gene Common Name Description Module membership
BSU02100 cypC fatty acid beta-hydroxylating cytochrome P450 (RefSeq) 10, 39
BSU02430 ybgJ glutaminase (RefSeq) 10, 305
BSU02480 gudP glucarate transporter (RefSeq) 10, 175
BSU05520 ydzH hypothetical protein (RefSeq) 10, 364
BSU05800 pbuE hypoxanthine efflux transporter (RefSeq) 10, 142
BSU05810 gmuB oligo-α-mannoside phosphotransferase system enzyme IIB (RefSeq) 10, 143
BSU05820 gmuA oligo-α-mannoside phosphotransferase system enzyme IIA (RefSeq) 10, 143
BSU05830 gmuC oligo-alpha-mannoside phosphotransferase system enzyme IIC (RefSeq) 10, 143
BSU05840 gmuD mannoside-phospho-beta-d-glucosidase (RefSeq) 10, 143
BSU05880 gmuG exported mannan endo-1,4-beta-mannosidase (RefSeq) 10, 143
BSU06590 yerD putative flavoenzyme (RefSeq) 10, 39
BSU06880 yesF hypothetical protein (RefSeq) 10, 361
BSU07000 yesR rhamnogalacturonan hydrolase (RefSeq) 10, 360
BSU07040 yesV putative integral inner membrane component (RefSeq) 10, 360
BSU07760 yfkT putative spore germination integral inner membrane protein (RefSeq) 59, 321
BSU07770 yfkS hypothetical protein (RefSeq) 59, 321
BSU07780 yfkR putative spore germination protein (RefSeq) 278, 321
BSU07790 yfkQ putative spore germination protein (RefSeq) 278, 321
BSU07800 treP phosphotransferase system (PTS) trehalose-specific enzyme IIBC component (RefSeq) 61, 321
BSU07810 treA trehalose-6-phosphate hydrolase (RefSeq) 61, 321
BSU07820 treR transcriptional regulator (GntR family) (RefSeq) 10, 321
BSU08100 acoR transcriptional regulator (RefSeq) 277, 321
BSU09190 yhcR non specific extracellular endonuclease cleaving RNA and DNA (RefSeq) 10, 305
BSU10270 yhfL long-chain-fatty-acid--CoA ligase (RefSeq) 10, 201
BSU11100 nprB extracellular neutral protease B (RefSeq) 10, 205
BSU17570 xynP putative H+-xyloside symporter (RefSeq) 321, 405
BSU17580 xynB xylan beta-1,4-xylosidase (RefSeq) 168, 321
BSU17960 yneK hypothetical protein (RefSeq) 10, 83
BSU29680 acsA acetyl-CoA synthetase (RefSeq) 134, 321
BSU29690 acuA protein acetyltransferase (RefSeq) 321, 330
BSU29700 acuB component of the acetoin degradation regulation pathway (RefSeq) 321, 330
BSU29710 acuC protein deacetylase (RefSeq) 321, 330
BSU34130 ganA arabinogalactan type I oligomer exo-hydrolase (beta-galactosidase, lactase) (RefSeq) 10, 152
BSU36510 amtB ammonium transporter (RefSeq) 10, 312
BSU38560 licH 6-phospho-beta-glucosidase (RefSeq) 186, 321
BSU38570 licA phosphotransferase system (PTS) lichenan-specific enzyme IIA component (RefSeq) 186, 321
BSU38580 licC phosphotransferase system (PTS) lichenan-specific enzyme IIC component (RefSeq) 186, 321
BSU38590 licB phosphotransferase system (PTS) lichenan-specific enzyme IIB component (RefSeq) 186, 321
BSU38780 yxkI putative membrane protease (RefSeq) 10, 95
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 BSU07820
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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