Organism : Bacillus subtilis | Module List :
BSU13670 mhqR

transcriptional regulator (MarR family) (RefSeq)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators 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 BSU13670
(Mouseover regulator name to see its description)

BSU13670 is regulated by 27 influences and regulates 8 modules.
Regulators for BSU13670 mhqR (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
BSU05970 154 tf
BSU06700 154 tf
BSU07820 154 tf
BSU08730 154 tf
BSU13670 154 tf
BSU15470 154 tf
BSU17450 154 tf
BSU22120 154 tf
BSU26730 154 tf
BSU35030 154 tf

Warning: BSU13670 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
5020 5.10e+01 agaaAaGgaggaaA
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5021 1.40e+04 ctCtCcCtgCC
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5256 3.50e-03 AAGGAtgAtt.GGA
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5257 1.00e-03 ACgcAccatCGgCgtgTaaTATaC
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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 BSU13670

BSU13670 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators 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 BSU13670

BSU13670 has total of 39 gene neighbors in modules 30, 154
Gene neighbors (39)
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
BSU04560 ddl D-alanyl-alanine synthetase A (RefSeq) 75, 154
BSU06700 yerO putative transcriptional regulator (TetR/AcrR family) (RefSeq) 75, 154
BSU06710 swrC transporter involved in surfactin self-resistance (RefSeq) 154, 227
BSU07170 yetI hypothetical protein (RefSeq) 154, 201
BSU07180 yetI hypothetical protein (RefSeq) 154, 294
BSU07240 yetN hypothetical protein (RefSeq) 75, 154
BSU07260 ltaSA exported glycerol phosphate lipoteichoic acid synthetase and anion-binding protein (RefSeq) 75, 154
BSU07420 yfmM putative ABC efflux transporter (ATP-binding protein) (RefSeq) 75, 154
BSU07430 yfmL putative ATP-dependent RNA helicase (RefSeq) 135, 154
BSU08910 yhbA putative iron-sulfur containing oxidoreductase subunit (RefSeq) 30, 154
BSU09470 yhdH putative sodium-dependent transporter (RefSeq) 67, 154
BSU09930 yhaM 3'-5' exoribonuclease YhaM (RefSeq) 154, 201
BSU10220 gltT proton/sodium-glutamate symport protein (RefSeq) 142, 154
BSU10630 addA ATP-dependent deoxyribonuclease (subunit A) (RefSeq) 20, 30
BSU13490 ykrL heat shock protein HtpX (RefSeq) 30, 47
BSU13650 eag putative small membrane protein (RefSeq) 47, 154
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
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
BSU18190 yngC putative integral inner membrane protein (RefSeq) 83, 154
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
BSU22510 ypjC putative integral inner membrane protein (RefSeq) 142, 154
BSU24900 rpmG 50S ribosomal protein L33 (RefSeq) 154, 395
BSU27920 obgE GTPase ObgE (RefSeq) 30, 227
BSU29170 fxsA FxsA (RefSeq) 30, 75
BSU29580 ytbJ thiamine biosynthesis protein ThiI (RefSeq) 30, 265
BSU37080 rho transcription termination factor Rho (RefSeq) 30, 199
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 BSU13670
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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