Organism : Bacillus subtilis | Module List :
BSU05330 aseR

transcriptional regulator (metals sensing ArsR-SmtB repressors family) (RefSeq)

CircVis
Functional Annotations (4)
Function System
Predicted 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 BSU05330
(Mouseover regulator name to see its description)

BSU05330 is regulated by 18 influences and regulates 16 modules.
Regulators for BSU05330 aseR (18)
Regulator Module Operator
BSU02680 14 tf
BSU02970 14 tf
BSU05330 14 tf
BSU05670 14 tf
BSU08990 14 tf
BSU09500 14 tf
BSU13880 14 tf
BSU24520 14 tf
BSU33740 14 tf
BSU35520 14 tf
BSU05330 161 tf
BSU05850 161 tf
BSU07390 161 tf
BSU09480 161 tf
BSU19200 161 tf
BSU25100 161 tf
BSU29000 161 tf
BSU40010 161 tf

Warning: BSU05330 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
4990 2.20e+01 AGGAgtg
Loader icon
4991 4.30e+02 AAcTcACCcTgCaTGACAAgC
Loader icon
5270 1.40e-03 ca.CagCcggC
Loader icon
5271 2.50e-01 AAaGTaCGTaCtTTTa.TtcT
Loader icon
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 BSU05330

BSU05330 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted 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 BSU05330

BSU05330 has total of 51 gene neighbors in modules 14, 161
Gene neighbors (51)
Gene Common Name Description Module membership
BSU01890 ybcL putative efflux transporter (RefSeq) 161, 405
BSU03020 ycgA putative integral inner membrane protein (RefSeq) 157, 161
BSU04230 ydaH putative integral inner membrane protein (RefSeq) 161, 177
BSU05300 ydeQ putative NAD(P)H oxidoreductase (RefSeq) 151, 161
BSU05330 aseR transcriptional regulator (metals sensing ArsR-SmtB repressors family) (RefSeq) 14, 161
BSU05340 ydfA putative metal-anion antiporter protein (RefSeq) 14, 38
BSU05680 ydgK putative efflux transporter (RefSeq) 14, 66
BSU06380 yebC putative integral inner membrane protein (RefSeq) 14, 66
BSU06580 yerC hypothetical protein (RefSeq) 161, 174
BSU07390 yfmP transcriptional regulator (MerR family) of metal efflux transporter expression (RefSeq) 161, 258
BSU07400 yfmO metal efflux transporter (RefSeq) 161, 270
BSU07710 yflE putative exported enzyme and anion transporter (RefSeq) 14, 409
BSU07830 yfkO NAD(P)H-flavin oxidoreductase (RefSeq) 19, 161
BSU08800 ygaK putative FAD-dependent oxido-reductase (RefSeq) 161, 174
BSU08990 yhbI putative transcriptional regulator (MarR family) (RefSeq) 14, 225
BSU09010 yhcA putative exporter (RefSeq) 14, 225
BSU09020 yhcB putative oxidoreductase associated to oxygen stress (RefSeq) 14, 66
BSU11090 yitR hypothetical protein (RefSeq) 71, 161
BSU11300 med positive regulator of comK (RefSeq) 14, 159
BSU11310 comZ putative late competence gene (RefSeq) 14, 67
BSU13110 purU formyltetrahydrofolate deformylase (RefSeq) 14, 67
BSU14950 ylbB putative oxidoreductase (RefSeq) 14, 161
BSU18810 yobA hypothetical protein (RefSeq) 161, 379
BSU23700 yqjX hypothetical protein (RefSeq) 161, 270
BSU23710 yqjW DNA polymerase IV (RefSeq) 161, 270
BSU25780 arsC arsenate reductase (RefSeq) 161, 249
BSU26640 yrdP putative oxidoreductase (RefSeq) 19, 161
BSU26650 czcD potassium/proton-divalent cation antiporter (RefSeq) 19, 161
BSU27210 yrhF hypothetical protein (RefSeq) 14, 66
BSU27540 yrvM putative enzyme of sulfur-containing coenzyme synthesis (RefSeq) 51, 161
BSU29030 ytcD putative transcriptional regulator (MarD family) (RefSeq) 157, 161
BSU29040 ytbD putative transporter (RefSeq) 4, 161
BSU29050 ytbE putative aldo/keto reductase (RefSeq) 4, 161
BSU29920 ytmP putative kinase/phosphotransferase (RefSeq) 14, 151
BSU30070 opuD glycine betaine transporter (RefSeq) 14, 151
BSU32120 yuzG hypothetical protein (RefSeq) 14, 163
BSU32130 guaC guanosine 5'-monophosphate oxidoreductase (RefSeq) 14, 377
BSU32880 yusP putative multidrug-efflux transporter (RefSeq) 14, 67
BSU33490 copB copper(I)-transporting ATPase (RefSeq) 161, 249
BSU33990 yvbU putative transcriptional regulator (LysR family) (RefSeq) 14, 66
BSU34410 yveG hypothetical protein (RefSeq) 161, 241
BSU34810 yvcD hypothetical protein (RefSeq) 14, 23
BSU35510 yvyE hypothetical protein (RefSeq) 14, 97
BSU35520 yvhJ putative membrane bound transcriptional regulator (RefSeq) 14, 97
BSU36230 ywqF UDP-glucose dehydrogenase (RefSeq) 14, 265
BSU36990 ywkF hypothetical protein (RefSeq) 14, 66
BSU37000 prmC glutamine methylase of release factor 1 (and perhaps others) at a GGQ site (RefSeq) 14, 265
BSU37010 prfA peptide chain release factor 1 (RefSeq) 14, 265
BSU38350 ywbE hypothetical protein (RefSeq) 127, 161
BSU38490 menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase (RefSeq) 14, 151
BSU40010 yxaD putative transcriptional regulator (MarR family) (RefSeq) 161, 270
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 BSU05330
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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