Organism : Bacillus subtilis | Module List :
BSU30790 menE

O-succinylbenzoic acid--CoA ligase (RefSeq)

CircVis
Functional Annotations (7)
Function System
Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II cog/ cog
o-succinylbenzoate-CoA ligase activity go/ molecular_function
menaquinone biosynthetic process go/ biological_process
Ubiquinone and other terpenoid-quinone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
menE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU30790
(Mouseover regulator name to see its description)

BSU30790 is regulated by 16 influences and regulates 0 modules.
Regulators for BSU30790 menE (16)
Regulator Module Operator
BSU05270 341 tf
BSU05700 341 tf
BSU09560 341 tf
BSU09690 341 tf
BSU27170 341 tf
BSU29000 341 tf
BSU31680 341 tf
BSU32140 341 tf
BSU36020 341 tf
BSU38450 341 tf
BSU38700 341 tf
BSU39850 341 tf
BSU02220 73 tf
BSU10840 73 tf
BSU38220 73 tf
BSU40050 73 tf

Warning: BSU30790 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
5102 1.50e+03 GGAaAcACAGGTGTATGG
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5103 2.00e+03 CAAGGAG
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5616 1.50e+02 aAaGcAGG
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5617 4.40e+01 AAccgaTgtA..G.aatgaa
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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 BSU30790

BSU30790 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II cog/ cog
o-succinylbenzoate-CoA ligase activity go/ molecular_function
menaquinone biosynthetic process go/ biological_process
Ubiquinone and other terpenoid-quinone biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
menE tigr/ tigrfam
Module neighborhood information for BSU30790

BSU30790 has total of 21 gene neighbors in modules 73, 341
Gene neighbors (21)
Gene Common Name Description Module membership
BSU03040 amyE alpha-amylase (RefSeq) 68, 341
BSU03160 ycgJ putative methyltransferase (RefSeq) 80, 341
BSU04330 mutT putative NTP pyrophosphohydrolase (RefSeq) 164, 341
BSU05440 nap carboxylesterase NP (RefSeq) 11, 341
BSU09710 yheI ABC transporter (ATP-binding protein) involved in the signalling pathway that activates KinA during sporulation initiation (RefSeq) 73, 356
BSU10050 ecsB ABC transporter (membrane protein) (RefSeq) 31, 341
BSU10060 ecsC putative hydrolase (RefSeq) 213, 341
BSU11080 yitQ hypothetical protein (RefSeq) 71, 341
BSU27180 yrhH putative methyltransferase (RefSeq) 341, 379
BSU29570 sspA small acid-soluble spore protein (alpha-type SASP) (RefSeq) 43, 73
BSU29980 ytjP dipeptidase PepV (RefSeq) 37, 341
BSU30780 menC O-succinylbenzoate-CoA synthase (RefSeq) 149, 341
BSU30790 menE O-succinylbenzoic acid--CoA ligase (RefSeq) 73, 341
BSU31480 yuxJ putative exporter (RefSeq) 238, 341
BSU33230 sigO alternative sigma factor (RefSeq) 111, 341
BSU34690 yvcS putative ABC transporter (permease) (RefSeq) 73, 325
BSU36000 alsD alpha-acetolactate decarboxylase (RefSeq) 237, 341
BSU36010 alsS acetolactate synthase (RefSeq) 237, 341
BSU38450 ywaE putative transcriptional regulator (MarR family) (RefSeq) 94, 341
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 BSU30790
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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