Organism : Bacillus subtilis | Module List :
BSU40050 gntR

transcriptional regulator (GntR family) (RefSeq)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU40050
(Mouseover regulator name to see its description)

BSU40050 is regulated by 22 influences and regulates 11 modules.
Regulators for BSU40050 gntR (22)
Regulator Module Operator
BSU00560 37 tf
BSU00700 37 tf
BSU01640 37 tf
BSU02680 37 tf
BSU03750 37 tf
BSU04680 37 tf
BSU05330 37 tf
BSU08370 37 tf
BSU11650 37 tf
BSU16600 37 tf
BSU17080 37 tf
BSU33740 37 tf
BSU33990 37 tf
BSU34180 37 tf
BSU35650 37 tf
BSU37580 37 tf
BSU40960 37 tf
BSU40990 37 tf
BSU02220 73 tf
BSU10840 73 tf
BSU38220 73 tf
BSU40050 73 tf

Warning: BSU40050 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
5034 1.30e+01 t..CCgcgAGAAAagAc.Tac
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5035 5.40e+01 TtTtttaAaAaCGtT
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5102 1.50e+03 GGAaAcACAGGTGTATGG
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5103 2.00e+03 CAAGGAG
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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 BSU40050

BSU40050 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
Module neighborhood information for BSU40050

BSU40050 has total of 33 gene neighbors in modules 37, 73
Gene neighbors (33)
Gene Common Name Description Module membership
BSU01140 ybaC putative proline iminopeptidase (RefSeq) 13, 37
BSU03750 yclJ two-component response regulator [YclK] (RefSeq) 37, 258
BSU03760 yclK two-component sensor histidine kinase [YclJ] (RefSeq) 37, 258
BSU08630 yfhQ A/G-specific adenine glycosylase or DNA-(apurinic or apyrimidinic site) lyase (RefSeq) 37, 314
BSU09710 yheI ABC transporter (ATP-binding protein) involved in the signalling pathway that activates KinA during sporulation initiation (RefSeq) 73, 356
BSU13090 ykkC efflux transporter (RefSeq) 37, 66
BSU16580 polC DNA polymerase III PolC (RefSeq) 37, 67
BSU18830 pps phosphoenolpyruvate synthase (RefSeq) 37, 53
BSU19160 yocC hypothetical protein (RefSeq) 37, 397
BSU22830 gpsA NAD(P)H-dependent glycerol-3-phosphate dehydrogenase (RefSeq) 37, 314
BSU23770 dsdA D-serine dehydratase (RefSeq) 1, 37
BSU23780 yqjQ putative metabolite dehydrogenase, NAD-binding (RefSeq) 1, 37
BSU23790 yqjP putative metal-dependent hydrolase (RefSeq) 37, 50
BSU24830 yqgT putative gamma-D-glutamyl-L-diamino acid endopeptidase (RefSeq) 37, 319
BSU27590 yrvI D-tyrosyl-tRNA(Tyr) deacylase (RefSeq) 37, 315
BSU28970 ytxB putative integral inner membrane protein (RefSeq) 37, 228
BSU29570 sspA small acid-soluble spore protein (alpha-type SASP) (RefSeq) 43, 73
BSU29980 ytjP dipeptidase PepV (RefSeq) 37, 341
BSU29990 pbuO hypoxanthine/guanine permease (RefSeq) 1, 37
BSU30790 menE O-succinylbenzoic acid--CoA ligase (RefSeq) 73, 341
BSU31100 ktrB potassium transporter ATPase (RefSeq) 37, 397
BSU33450 helD DNA 3'-5' helicase IV (RefSeq) 1, 37
BSU33500 copA copper transporter ATPase (RefSeq) 37, 50
BSU33510 copZ copper insertion chaperone and transporter component (RefSeq) 37, 50
BSU34690 yvcS putative ABC transporter (permease) (RefSeq) 73, 325
BSU36620 ywnB putative oxidoreductase (RefSeq) 37, 365
BSU36950 ywlC putative ribosome maturation factor; RNA binding protein (RefSeq) 37, 233
BSU37570 mmr toxic compound efflux transporter (RefSeq) 37, 50
BSU38290 thiE thiamine-phosphate pyrophosphorylase (RefSeq) 37, 262
BSU38300 thiM hydroxyethylthiazole kinase (RefSeq) 37, 262
BSU38840 yxkD efflux transporter (RefSeq) 37, 293
BSU40050 gntR transcriptional regulator (GntR family) (RefSeq) 37, 73
BSU40070 gntP gluconate permease (RefSeq) 73, 284
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 BSU40050
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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