Organism : Bacillus subtilis | Module List :
BSU08990 yhbI

putative 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 BSU08990
(Mouseover regulator name to see its description)

BSU08990 is regulated by 17 influences and regulates 11 modules.
Regulators for BSU08990 yhbI (17)
Regulator Module Operator
BSU00800 225 tf
BSU08990 225 tf
BSU10150 225 tf
BSU15690 225 tf
BSU25760 225 tf
BSU32870 225 tf
BSU40410 225 tf
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

Warning: BSU08990 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
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4991 4.30e+02 AAcTcACCcTgCaTGACAAgC
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5394 6.30e+00 aAacAaGaaaAAAa.aAAat
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5395 3.30e+03 CCaT.TCaGc
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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 BSU08990

BSU08990 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 BSU08990

BSU08990 has total of 49 gene neighbors in modules 14, 225
Gene neighbors (49)
Gene Common Name Description Module membership
BSU00270 yaaO putative lysine decarboxylase (RefSeq) 54, 225
BSU00280 tmk thymidylate kinase (RefSeq) 54, 225
BSU00320 yaaT hypothetical protein (RefSeq) 54, 225
BSU00340 yabB putative methyltransferase (RefSeq) 225, 288
BSU00350 yazA GIY-YIG nuclease superfamily protein (RefSeq) 225, 288
BSU00360 yabC putative methyltransferase (RefSeq) 225, 288
BSU00740 pabB 4-amino-4-deoxychorismate synthase (para-aminobenzoate synthase) (RefSeq) 97, 225
BSU00750 pabA para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II (RefSeq) 97, 225
BSU00760 pabC 4-amino-4-deoxychorismate lyase (RefSeq) 97, 225
BSU00770 sul dihydropteroate synthase (RefSeq) 97, 225
BSU00780 folB dihydroneopterin aldolase (RefSeq) 97, 225
BSU00790 folK 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase (RefSeq) 97, 225
BSU00800 yazB putative transcriptional regulator (RefSeq) 97, 225
BSU00810 dusB tRNA-dihydrouridine synthase B (RefSeq) 97, 225
BSU00820 lysS lysyl-tRNA synthetase (RefSeq) 97, 225
BSU01760 ybbR hypothetical protein (RefSeq) 225, 265
BSU01770 glmM phosphoglucosamine mutase (RefSeq) 225, 265
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
BSU07710 yflE putative exported enzyme and anion transporter (RefSeq) 14, 409
BSU08990 yhbI putative transcriptional regulator (MarR family) (RefSeq) 14, 225
BSU09000 yhbJ putative integral inner membrane protein; putative exporter subunit (RefSeq) 66, 225
BSU09010 yhcA putative exporter (RefSeq) 14, 225
BSU09020 yhcB putative oxidoreductase associated to oxygen stress (RefSeq) 14, 66
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
BSU15660 yloC hypothetical protein (RefSeq) 225, 288
BSU25140 cshB ATP-dependent RNA helicase; cold shock (RefSeq) 204, 225
BSU27210 yrhF hypothetical protein (RefSeq) 14, 66
BSU27600 relA GTP pyrophosphokinase (RelA/SpoT) (RefSeq) 225, 293
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
BSU32870 yusO putative transcriptional regulator (MarR family) (RefSeq) 97, 225
BSU32880 yusP putative multidrug-efflux transporter (RefSeq) 14, 67
BSU33990 yvbU putative transcriptional regulator (LysR family) (RefSeq) 14, 66
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
BSU38490 menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase (RefSeq) 14, 151
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 BSU08990
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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