Organism : Bacillus subtilis | Module List :
BSU06700 yerO

putative transcriptional regulator (TetR/AcrR family) (RefSeq)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU06700
(Mouseover regulator name to see its description)

BSU06700 is regulated by 24 influences and regulates 18 modules.
Regulators for BSU06700 yerO (24)
Regulator Module Operator
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
BSU01070 75 tf
BSU06700 75 tf
BSU07820 75 tf
BSU13670 75 tf
BSU13880 75 tf
BSU15470 75 tf
BSU16470 75 tf
BSU21700 75 tf
BSU24020 75 tf
BSU26220 75 tf
BSU26340 75 tf
BSU29690 75 tf
BSU34170 75 tf
BSU35030 75 tf

Warning: BSU06700 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
5106 1.80e+04 TAaAaaaAaaAGGa
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5107 1.50e+03 AAatGGAAGG
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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 BSU06700

BSU06700 is enriched for 5 functions in 3 categories.
Module neighborhood information for BSU06700

BSU06700 has total of 37 gene neighbors in modules 75, 154
Gene neighbors (37)
Gene Common Name Description Module membership
BSU02290 psd phosphatidylserine decarboxylase (RefSeq) 75, 227
BSU02300 ybfN hypothetical protein (RefSeq) 75, 294
BSU04560 ddl D-alanyl-alanine synthetase A (RefSeq) 75, 154
BSU05910 ydiB putative ATPase or kinase UPF0079 (RefSeq) 75, 312
BSU05940 gcp putative DNA-binding/iron metalloprotein/AP endonuclease (RefSeq) 75, 135
BSU06630 yerH putative lipoprotein (RefSeq) 75, 227
BSU06700 yerO putative transcriptional regulator (TetR/AcrR family) (RefSeq) 75, 154
BSU06710 swrC transporter involved in surfactin self-resistance (RefSeq) 154, 227
BSU06750 yefC putative resolvase (RefSeq) 75, 199
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
BSU07650 yflK putative sulfur carrier (RefSeq) 75, 135
BSU08910 yhbA putative iron-sulfur containing oxidoreductase subunit (RefSeq) 30, 154
BSU09090 yhcI putative ABC transporter (permease) (RefSeq) 75, 142
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
BSU13650 eag putative small membrane protein (RefSeq) 47, 154
BSU13670 mhqR transcriptional regulator (MarR family) (RefSeq) 30, 154
BSU13720 queC pre-queuosine 0 synthase (RefSeq) 75, 95
BSU14210 ykuT putative small-conductance mechanosensitive channel (RefSeq) 30, 154
BSU17460 glnA glutamine synthetase (RefSeq) 30, 75
BSU17780 yndG hypothetical protein (RefSeq) 75, 244
BSU17800 yndJ putative integral inner membrane protein (RefSeq) 75, 244
BSU18120 alsT amino acid carrier protein (RefSeq) 75, 190
BSU18190 yngC putative integral inner membrane protein (RefSeq) 83, 154
BSU22510 ypjC putative integral inner membrane protein (RefSeq) 142, 154
BSU24900 rpmG 50S ribosomal protein L33 (RefSeq) 154, 395
BSU25610 yqeM hypothetical protein (RefSeq) 75, 227
BSU27550 aspS aspartyl-tRNA synthetase (RefSeq) 75, 300
BSU29170 fxsA FxsA (RefSeq) 30, 75
BSU34110 rsbP serine phosphatase (RefSeq) 75, 132
BSU36250 ptkA protein tyrosine kinase (RefSeq) 75, 395
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 BSU06700
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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