Organism : Bacillus subtilis | Module List :
BSU02680 lmrA

transcriptional repressor of lmrAB and yxaGH operons (RefSeq)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU02680
(Mouseover regulator name to see its description)

BSU02680 is regulated by 16 influences and regulates 28 modules.
Regulators for BSU02680 lmrA (16)
Regulator Module Operator
BSU01010 69 tf
BSU01070 69 tf
BSU02680 69 tf
BSU03080 69 tf
BSU05330 69 tf
BSU15970 69 tf
BSU32870 69 tf
BSU33990 69 tf
BSU36440 69 tf
BSU01010 271 tf
BSU02680 271 tf
BSU15970 271 tf
BSU27520 271 tf
BSU33080 271 tf
BSU33740 271 tf
BSU38600 271 tf

Warning: BSU02680 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
5094 1.20e+02 AgGcGG.A
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5095 2.40e+03 tCTCCA
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5480 1.30e+02 ACtGaAAAAaAcagg
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5481 4.00e+03 AGGaGGgA
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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 BSU02680

BSU02680 is enriched for 5 functions in 3 categories.
Module neighborhood information for BSU02680

BSU02680 has total of 32 gene neighbors in modules 69, 271
Gene neighbors (32)
Gene Common Name Description Module membership
BSU02280 ybfM putative membrane phosphatase (RefSeq) 69, 212
BSU02670 lmrB efflux transporter; drug-export protein (RefSeq) 69, 271
BSU02680 lmrA transcriptional repressor of lmrAB and yxaGH operons (RefSeq) 69, 271
BSU02860 adcC Zn(II) transporter (ATP-binding protein) (RefSeq) 271, 409
BSU02870 adcB high affinity Zn(II) ABC transporter (permease) (RefSeq) 271, 409
BSU03652 BSU03652 None 69, 184
BSU06350 yebA hypothetical protein (RefSeq) 67, 271
BSU06720 yerQ putative lipid kinase (RefSeq) 271, 397
BSU07940 yfkC putative mechanosensitive ion channel (RefSeq) 69, 397
BSU09965 BSU09965 None 132, 271
BSU13500 ktrD K+-transporting ATPase (RefSeq) 271, 397
BSU19450 rsbRC Component of the piezosome (stressosome) (RefSeq) 227, 271
BSU22150 ypvA putative ATP-dependent helicase (RefSeq) 271, 319
BSU22170 ypsC putative methylase with RNA interaction domain (RefSeq) 265, 271
BSU30050 ytgP putative enzyme involved in polysaccharide biosynthesis (RefSeq) 271, 397
BSU30490 ytqB putative RNA methylase (RefSeq) 271, 319
BSU31945 BSU31945 None 69, 287
BSU36280 ywqA putative ATP-binding SNF2 helicase or protein kinase (RefSeq) 190, 271
BSU40440 dnaC replicative DNA helicase (RefSeq) 69, 271
VIMSS36728 VIMSS36728 None 69, 117
VIMSS36891 VIMSS36891 None 69, 271
VIMSS37328 VIMSS37328 None 69, 211
VIMSS37529 VIMSS37529 None 69, 271
VIMSS37621 VIMSS37621 None 69, 211
VIMSS38221 VIMSS38221 None 69, 184
VIMSS38484 VIMSS38484 None 67, 69
VIMSS39235 VIMSS39235 None 69, 98
VIMSS39723 VIMSS39723 None 72, 271
VIMSS39730 VIMSS39730 None 69, 184
VIMSS39733 VIMSS39733 None 69, 98
VIMSS39734 VIMSS39734 None 69, 407
VIMSS40451 VIMSS40451 None 69, 120
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 BSU02680
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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