Organism : Bacillus subtilis | Module List :
VIMSS39838

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VIMSS39838
(Mouseover regulator name to see its description)

VIMSS39838 is regulated by 30 influences and regulates 0 modules.
Regulators for VIMSS39838 (30)
Regulator Module Operator
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
BSU00230 100 tf
BSU03470 100 tf
BSU04460 100 tf
BSU05320 100 tf
BSU08410 100 tf
BSU10420 100 tf
BSU10840 100 tf
BSU12370 100 tf
BSU14730 100 tf
BSU18460 100 tf
BSU29030 100 tf
BSU29740 100 tf
BSU36300 100 tf
BSU40870 100 tf

Warning: VIMSS39838 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
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5011 6.30e-02 ACacCCcTTaccaaaCtGTCA
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5154 9.50e-01 ctGAAAGGAGaGg
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5155 6.30e+02 cCAGaAAgtAT
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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 VIMSS39838

Warning: No Functional annotations were found!

Module neighborhood information for VIMSS39838

VIMSS39838 has total of 33 gene neighbors in modules 24, 100
Gene neighbors (33)
Gene Common Name Description Module membership
BSU01845 BSU01845 None 24, 164
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
BSU03420 nin inhibitor of the DNA degrading activity of NucA (competence) (RefSeq) 100, 394
BSU03430 nucA endonuclease (RefSeq) 100, 394
BSU11530 coiA protein involved in establishment of DNA transport in competence (RefSeq) 100, 394
BSU24660 yqzE hypothetical protein (RefSeq) 100, 394
BSU24670 comGG component of the DNA transport platform (RefSeq) 100, 394
BSU24680 comGF component of the DNA transport platform (RefSeq) 100, 394
BSU24690 comGE component of the DNA transport platform (RefSeq) 100, 394
BSU24700 comGD membrane component of the DNA transport platform (RefSeq) 100, 394
BSU24710 comGC pilin-like component of the DNA transport membrane platform (RefSeq) 100, 394
BSU24720 comGB membrane platform component of the DNA transport machinery (RefSeq) 100, 394
BSU24730 comGA membrane associated factor for DNA competence (RefSeq) 100, 394
BSU25590 comEA membrane bound high-affinity DNA-binding receptor (RefSeq) 100, 394
BSU26075 BSU26075 None 24, 176
BSU33221 BSU33221 None 100, 215
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
BSU35470 comFA helicase competence protein (RefSeq) 100, 394
BSU36310 ssbB single-strand DNA-binding protein (RefSeq) 100, 394
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 VIMSS39838
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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