Organism : Bacillus subtilis | Module List :
BSU02370 ybgA

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 BSU02370
(Mouseover regulator name to see its description)

BSU02370 is regulated by 22 influences and regulates 12 modules.
Regulators for BSU02370 ybgA (22)
Regulator Module Operator
BSU02370 199 tf
BSU04820 199 tf
BSU05420 199 tf
BSU06700 199 tf
BSU35030 199 tf
BSU37080 199 tf
BSU01810 24 tf
BSU02370 24 tf
BSU03080 24 tf
BSU04100 24 tf
BSU08410 24 tf
BSU09060 24 tf
BSU17450 24 tf
BSU19050 24 tf
BSU23120 24 tf
BSU23520 24 tf
BSU25200 24 tf
BSU27170 24 tf
BSU31530 24 tf
BSU33080 24 tf
BSU33840 24 tf
BSU34060 24 tf

Warning: BSU02370 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
5010 6.60e-02 AAaAAGtaTACAAatctTTcAtAT
Loader icon
5011 6.30e-02 ACacCCcTTaccaaaCtGTCA
Loader icon
5342 6.70e-01 TtTtatAGgagGaga
Loader icon
5343 1.90e+03 ACCCCaaATTTTTCtTtACTT
Loader icon
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 BSU02370

BSU02370 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 BSU02370

BSU02370 has total of 43 gene neighbors in modules 24, 199
Gene neighbors (43)
Gene Common Name Description Module membership
BSU01845 BSU01845 None 24, 164
BSU02060 ybxG putative amino acid permease (RefSeq) 95, 199
BSU02350 nagP phosphotransferase system (PTS) glucosamine-specific enzyme IICBA component (RefSeq) 24, 240
BSU02360 nagBB glucosamine-6-phosphate isomerase (RefSeq) 24, 240
BSU02370 ybgA putative transcriptional regulator (GntR family) (RefSeq) 24, 199
BSU02400 ybgF putative aminoacid permease (RefSeq) 199, 240
BSU05030 yddM putative helicase; mobile element region (RefSeq) 47, 199
BSU05410 ydfH two-component sensor histidine kinase [YdfI] (RefSeq) 199, 244
BSU05420 ydfI two-component response regulator [YdfH] (RefSeq) 199, 255
BSU06110 ydjA BsuM intrinsic DNA restriction component (RefSeq) 128, 199
BSU06740 yefB putative site-specific recombinase / invertase (RefSeq) 178, 199
BSU06750 yefC putative resolvase (RefSeq) 75, 199
BSU07190 yezD hypothetical protein (RefSeq) 95, 199
BSU07210 yetK putative efflux transporter (RefSeq) 95, 199
BSU13570 mtnU putative hydrolase (RefSeq) 183, 199
BSU13580 ykrV transaminase (RefSeq) 28, 199
BSU17330 miaA tRNA delta(2)-isopentenylpyrophosphate transferase (RefSeq) 135, 199
BSU18970 yobI putative NTPase with transmembrane helices (RefSeq) 135, 199
BSU22080 ypwA metal-dependent carboxypeptidase (RefSeq) 128, 199
BSU22180 ypsB cell division protein GpsB (RefSeq) 47, 199
BSU22200 cotD spore coat protein (inner) (RefSeq) 30, 199
BSU22330 ypoC hypothetical protein (RefSeq) 67, 199
BSU26075 BSU26075 None 24, 176
BSU26748 yrdD 89, 199
BSU27100 yrhP putative efflux transporter (RefSeq) 199, 255
BSU27890 nadR transcriptional repressor of de novo NAD biosynthesis (RefSeq) 15, 199
BSU27900 pheA prephenate dehydratase (RefSeq) 199, 313
BSU33700 opuBD choline ABC transporter (permease) (RefSeq) 24, 137
BSU33710 opuBC choline ABC transporter (choline-binding lipoprotein) (RefSeq) 24, 137
BSU33720 opuBB choline ABC transporter (permease) (RefSeq) 24, 137
BSU33730 opuBA choline ABC transporter (ATP-binding protein) (RefSeq) 24, 261
BSU33800 opuCD glycine betaine/carnitine/choline/choline sulfate ABC transporter (permease) (RefSeq) 24, 261
BSU33810 opuCC glycine betaine/carnitine/choline/choline sulfate ABC transporter (osmoprotectant-binding lipoprotein) (RefSeq) 24, 261
BSU33820 opuCB glycine betaine/carnitine/choline/choline sulfate ABC transporter (permease) (RefSeq) 24, 261
BSU33830 opuCA glycine betaine/carnitine/choline/choline sulfate ABC transporter (ATP-binding protein) (RefSeq) 24, 261
BSU33840 yvbF putative transcriptional regulator (RefSeq) 24, 261
BSU33880 yvbJ hypothetical protein (RefSeq) 199, 313
BSU35680 ggaB poly(glucosyl N-acetylgalactosamine 1-phosphate) glucosyltransferase (RefSeq) 32, 199
BSU37080 rho transcription termination factor Rho (RefSeq) 30, 199
VIMSS37138 VIMSS37138 None 24, 117
VIMSS37306 VIMSS37306 None 24, 164
VIMSS37638 VIMSS37638 None 24, 127
VIMSS39838 VIMSS39838 None 24, 100
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 BSU02370
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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