Organism : Bacillus subtilis | Module List :
BSU17450 glnR

transcriptional regulator (nitrogen metabolism) (RefSeq)

CircVis
Functional Annotations (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU17450
(Mouseover regulator name to see its description)

BSU17450 is regulated by 27 influences and regulates 7 modules.
Regulators for BSU17450 glnR (27)
Regulator Module Operator
BSU01070 30 tf
BSU01080 30 tf
BSU02370 30 tf
BSU05330 30 tf
BSU06700 30 tf
BSU08730 30 tf
BSU13670 30 tf
BSU13870 30 tf
BSU17450 30 tf
BSU17590 30 tf
BSU17850 30 tf
BSU20780 30 tf
BSU21020 30 tf
BSU22120 30 tf
BSU27320 30 tf
BSU36600 30 tf
BSU37080 30 tf
BSU02000 294 tf
BSU02160 294 tf
BSU05970 294 tf
BSU06700 294 tf
BSU07820 294 tf
BSU09480 294 tf
BSU13870 294 tf
BSU17850 294 tf
BSU35030 294 tf
BSU36600 294 tf
Regulated by BSU17450 (7)
Module Residual Genes
24 0.42 18
30 0.36 23
78 0.41 25
154 0.30 19
165 0.43 7
241 0.43 23
264 0.43 6
Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
5020 5.10e+01 agaaAaGgaggaaA
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5021 1.40e+04 ctCtCcCtgCC
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5526 2.50e-03 AaaAAAGGgGagt
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5527 5.10e+00 gtTCgcTctgcaggc
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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 BSU17450

BSU17450 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted transcriptional regulators cog/ cog
nucleotide binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BSU17450

BSU17450 has total of 42 gene neighbors in modules 30, 294
Gene neighbors (42)
Gene Common Name Description Module membership
BSU01360 secY preprotein translocase subunit SecY (RefSeq) 30, 140
BSU01380 mapA methionine aminopeptidase (RefSeq) 30, 140
BSU01470 ybaF putative permease (RefSeq) 30, 176
BSU01780 glmS glucosamine--fructose-6-phosphate aminotransferase (RefSeq) 30, 283
BSU02300 ybfN hypothetical protein (RefSeq) 75, 294
BSU02850 adcA Zn(II)-binding lipoprotein (RefSeq) 294, 395
BSU05510 ydfQ putative thioredoxin or thiol-disulfide isomerase (RefSeq) 95, 294
BSU05690 ydhB putative integral inner membrane protein (RefSeq) 270, 294
BSU06370 pbuG hypoxanthine/guanine permease (RefSeq) 190, 294
BSU06660 opuE proline transporter (RefSeq) 142, 294
BSU07180 yetI hypothetical protein (RefSeq) 154, 294
BSU07720 yflD hypothetical protein (RefSeq) 95, 294
BSU08910 yhbA putative iron-sulfur containing oxidoreductase subunit (RefSeq) 30, 154
BSU09480 yhdI putative PLP-dependent transcriptional regulator (RefSeq) 95, 294
BSU10630 addA ATP-dependent deoxyribonuclease (subunit A) (RefSeq) 20, 30
BSU13440 ykoY putative transporter (RefSeq) 178, 294
BSU13490 ykrL heat shock protein HtpX (RefSeq) 30, 47
BSU13670 mhqR transcriptional regulator (MarR family) (RefSeq) 30, 154
BSU14210 ykuT putative small-conductance mechanosensitive channel (RefSeq) 30, 154
BSU16140 xerC site-specific tyrosine recombinase XerC (RefSeq) 30, 227
BSU17290 ebrB small multidrug efflux transporter (RefSeq) 38, 294
BSU17310 ymaG putative cell wall associated protein (RefSeq) 294, 358
BSU17370 nrdI ribonucleotide reductase stimulatory protein (RefSeq) 30, 227
BSU17380 nrdE ribonucleotide-diphosphate reductase subunit alpha (RefSeq) 30, 227
BSU17390 nrdF ribonucleotide-diphosphate reductase subunit beta (RefSeq) 30, 227
BSU17400 ymaB putative enzyme involved in deoxyribonucleotide synthesis (RefSeq) 30, 227
BSU17450 glnR transcriptional regulator (nitrogen metabolism) (RefSeq) 30, 294
BSU17460 glnA glutamine synthetase (RefSeq) 30, 75
BSU17880 ynzC hypothetical protein (RefSeq) 244, 294
BSU18060 yneR hypothetical protein (RefSeq) 20, 294
BSU19390 yojN putative nitric-oxide reductase (RefSeq) 30, 227
BSU22200 cotD spore coat protein (inner) (RefSeq) 30, 199
BSU22210 yprB putative nucleic acid binding enzyme (RefSeq) 30, 223
BSU25010 yqgE putative efflux transporter (RefSeq) 174, 294
BSU26110 yqbH conserved hypothetical protein; skin element (RefSeq) 175, 294
BSU27920 obgE GTPase ObgE (RefSeq) 30, 227
BSU28320 ysnD hypothetical protein (RefSeq) 108, 294
BSU29170 fxsA FxsA (RefSeq) 30, 75
BSU29580 ytbJ thiamine biosynthesis protein ThiI (RefSeq) 30, 265
BSU34400 padC phenolic acid decarboxylase (RefSeq) 95, 294
BSU37080 rho transcription termination factor Rho (RefSeq) 30, 199
BSU37200 uvsE putative UV damage endonuclease (RefSeq) 26, 294
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 BSU17450
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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