Organism : Bacillus subtilis | Module List :
BSU03890 gabR

transcriptional regulator (GntR/MocR family) with PLP binding site (RefSeq)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
catalytic activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
pyridoxal phosphate binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU03890
(Mouseover regulator name to see its description)

BSU03890 is regulated by 30 influences and regulates 20 modules.
Regulators for BSU03890 gabR (30)
Regulator Module Operator
BSU02000 360 tf
BSU02320 360 tf
BSU03890 360 tf
BSU06960 360 tf
BSU07820 360 tf
BSU08100 360 tf
BSU26320 360 tf
BSU30150 360 tf
BSU37290 360 tf
BSU00800 175 tf
BSU02070 175 tf
BSU02160 175 tf
BSU03890 175 tf
BSU05290 175 tf
BSU05370 175 tf
BSU06540 175 tf
BSU09500 175 tf
BSU15690 175 tf
BSU16470 175 tf
BSU17590 175 tf
BSU21700 175 tf
BSU26320 175 tf
BSU26430 175 tf
BSU32920 175 tf
BSU33230 175 tf
BSU33970 175 tf
BSU35520 175 tf
BSU36600 175 tf
BSU40010 175 tf
BSU40800 175 tf

Warning: BSU03890 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
5298 2.80e-04 cactCCttTTt
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5299 6.50e+02 ccGcatccGcGCatacTAtAgc
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5644 4.50e-02 GTaAGCgcTttCt.taaagg
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5645 5.70e+01 GGggaaAttCA
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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 BSU03890

BSU03890 is enriched for 6 functions in 3 categories.
Module neighborhood information for BSU03890

BSU03890 has total of 42 gene neighbors in modules 175, 360
Gene neighbors (42)
Gene Common Name Description Module membership
BSU01990 ybdG putative hydrolase/transferase (RefSeq) 89, 360
BSU02000 ybdJ two-component response regulator [YbdK] (RefSeq) 312, 360
BSU02160 ybfA hypothetical protein (RefSeq) 175, 358
BSU02320 ybfP putative transcriptional regulator (AraC/XylS family) (RefSeq) 8, 360
BSU02480 gudP glucarate transporter (RefSeq) 10, 175
BSU03890 gabR transcriptional regulator (GntR/MocR family) with PLP binding site (RefSeq) 175, 360
BSU05310 ydeR putative efflux transporter (RefSeq) 175, 305
BSU05360 ydfC putative permease (RefSeq) 88, 175
BSU05430 ydfJ putative proton metabolite efflux transporter (RefSeq) 175, 305
BSU05560 ydgA hypothetical protein (RefSeq) 175, 358
BSU05720 ydhE putative glycosyltransferase (RefSeq) 285, 360
BSU06220 ydjJ putative membrane associated potassium channel (RefSeq) 175, 364
BSU06970 yesO pectin degradation byproducts-binding lipoprotein (RefSeq) 143, 360
BSU06980 yesP rhamnogalacturonan permease (RefSeq) 143, 360
BSU06990 yesQ rhamnogalacturonan permease (RefSeq) 360, 371
BSU07000 yesR rhamnogalacturonan hydrolase (RefSeq) 10, 360
BSU07020 rhgT rhamnogalacturonan acetylesterase (RefSeq) 143, 360
BSU07040 yesV putative integral inner membrane component (RefSeq) 10, 360
BSU07050 yesW polysaccharide lyase; lipoprotein (RefSeq) 360, 372
BSU07060 yesX polysaccharide lyase (RefSeq) 360, 372
BSU07090 yetA putative enzyme (RefSeq) 143, 360
BSU07110 lplB putative ABC transporter (permease) (RefSeq) 360, 372
BSU07120 lplC putative ABC transporter (permease) (RefSeq) 143, 360
BSU07250 yetO putative cytochrome P450 CYP102A2 (RefSeq) 175, 387
BSU07910 yfkF putative efflux transporter (RefSeq) 175, 387
BSU08280 yfiI putative oxidoreductase (RefSeq) 360, 371
BSU08330 yfiN putative ABC transporter (permease) (RefSeq) 175, 371
BSU09740 yheF hypothetical protein; orphan (RefSeq) 39, 175
BSU10580 yhjO hypothetical protein (RefSeq) 175, 371
BSU10970 yitF putative enolase superfamily enzyme (RefSeq) 175, 326
BSU11260 yjzC hypothetical protein (RefSeq) 175, 282
BSU13050 ykzH hypothetical protein (RefSeq) 88, 175
BSU23930 yqjC putative lyase (RefSeq) 175, 387
BSU26100 yqbI conserved hypothetical protein; skin element (RefSeq) 130, 175
BSU26110 yqbH conserved hypothetical protein; skin element (RefSeq) 175, 294
BSU30100 yteT putative dehydrogenase of rhamnogalaturonan degradation (RefSeq) 360, 371
BSU30110 yteS putative lipoprotein required for rhamnogalaturonan degradation (RefSeq) 360, 371
BSU30120 yteR unsaturated rhamnogalacturonyl hydrolase (RefSeq) 360, 371
BSU33550 yvaC putative integral inner membrane protein (RefSeq) 175, 358
BSU34190 yvfH putative lactate permease (RefSeq) 330, 360
BSU36140 ywqO hypothetical protein (RefSeq) 84, 175
BSU39970 yxaH putative integral inner membrane protein (RefSeq) 142, 175
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 BSU03890
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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