Organism : Bacillus subtilis | Module List :
BSU39770 iolR

transcriptional regulator (DeoR family) (RefSeq)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators of sugar metabolism 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 BSU39770
(Mouseover regulator name to see its description)

BSU39770 is regulated by 15 influences and regulates 3 modules.
Regulators for BSU39770 iolR (15)
Regulator Module Operator
BSU09520 402 tf
BSU14730 402 tf
BSU18460 402 tf
BSU27110 402 tf
BSU31070 402 tf
BSU31530 402 tf
BSU35840 402 tf
BSU05700 323 tf
BSU10560 323 tf
BSU30020 323 tf
BSU33790 323 tf
BSU36020 323 tf
BSU38600 323 tf
BSU38700 323 tf
BSU39770 323 tf

Warning: BSU39770 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
5584 7.60e-04 gAAAAaGaG.GgaaA
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5585 5.70e+00 ATcTTTtCATtTTtATcCca
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5712 1.30e+02 gAAGGA
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5713 3.30e+04 CTGGACGg
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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 BSU39770

BSU39770 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators of sugar metabolism 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 BSU39770

BSU39770 has total of 41 gene neighbors in modules 323, 402
Gene neighbors (41)
Gene Common Name Description Module membership
BSU02970 yceK putative transcriptional regulator (ArsR family) (RefSeq) 378, 402
BSU03090 ycgF putative aminoacid export permease (RefSeq) 291, 402
BSU04760 ydcG hypothetical protein (RefSeq) 54, 323
BSU05700 ydhC putative transcriptional regulator (GntR family) (RefSeq) 270, 323
BSU07640 yflL acylphosphatase (RefSeq) 310, 323
BSU10000 yhaH putative membrane protein; acid tolerance protein (RefSeq) 323, 354
BSU11490 yjbC putative thiol oxidation management factor; putative acetyltransferase (RefSeq) 215, 323
BSU12140 yjgA hypothetical protein (RefSeq) 378, 402
BSU12900 htrA membrane bound serine protease Do, quality control protease (heat-shock protein) (RefSeq) 310, 323
BSU12910 proG pyrroline-5-carboxylate reductase (RefSeq) 233, 323
BSU14690 yktD hypothetical protein (RefSeq) 177, 402
BSU14730 ylaC RNA polymerase ECF-type sigma factor (RefSeq) 274, 402
BSU14830 ylaM glutaminase (RefSeq) 258, 323
BSU15390 sepF cell division machinery factor (RefSeq) 237, 402
BSU15420 divIVA cell-division initiation protein (RefSeq) 64, 402
BSU17730 yndB hypothetical protein (RefSeq) 258, 323
BSU18460 gltC transcriptional regulator (LysR family) (RefSeq) 23, 402
BSU18530 yoaA putative N-acetyltransferase (RefSeq) 91, 323
BSU19310 dhaS putative aldehyde dehydrogenase (RefSeq) 217, 323
BSU22950 ypdA putative FAD-dependent disulfide oxidoreductase (RefSeq) 82, 402
BSU22990 ypbF hypothetical protein (RefSeq) 377, 402
BSU24850 glcK glucose kinase (RefSeq) 54, 323
BSU24860 yqgQ hypothetical protein (RefSeq) 54, 323
BSU26560 yrkC putative dioxygenase; cupin family (RefSeq) 323, 379
BSU30310 ytwF putative sulfur transferase (RefSeq) 258, 323
BSU30330 ytvB putative conserved membrane protein (RefSeq) 55, 323
BSU30700 rpmE2 50S ribosomal protein L31 type B (RefSeq) 377, 402
BSU31120 lytG exoglucosaminidase (RefSeq) 197, 402
BSU31490 pbpD penicillin-binding protein 4 (RefSeq) 102, 402
BSU31500 yuxK hypothetical protein (RefSeq) 233, 402
BSU33000 htrB HtrA-like serine protease (RefSeq) 54, 323
BSU35180 csbA hypothetical protein (RefSeq) 215, 323
BSU35660 mnaA UDP-N-acetylmannosamine 2-epimerase (RefSeq) 102, 402
BSU35690 ggaA poly(glucosyl N-acetylgalactosamine 1-phosphate) glucosyltransferase (RefSeq) 67, 402
BSU38070 sacT transcriptional antiterminator (RefSeq) 12, 323
BSU39330 abnB arabinan endo-1,5-alpha-L-arabinosidase (RefSeq) 136, 323
BSU39770 iolR transcriptional regulator (DeoR family) (RefSeq) 323, 402
BSU39780 iolS aldo-keto reductase (RefSeq) 259, 323
BSU40060 gntK gluconate kinase (RefSeq) 54, 323
BSU40690 yybC putative integral inner membrane protein (RefSeq) 11, 402
BSU40750 yyaQ hypothetical protein (RefSeq) 310, 323
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 BSU39770
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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