Organism : Bacillus subtilis | Module List :
BSU40540 yybR

putative transcriptional regulator (RefSeq)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU40540
(Mouseover regulator name to see its description)

BSU40540 is regulated by 17 influences and regulates 9 modules.
Regulators for BSU40540 yybR (17)
Regulator Module Operator
BSU04060 249 tf
BSU13760 249 tf
BSU25810 249 tf
BSU30020 249 tf
BSU34480 249 tf
BSU40540 249 tf
BSU03620 109 tf
BSU05270 109 tf
BSU05850 109 tf
BSU09430 109 tf
BSU10510 109 tf
BSU13150 109 tf
BSU13760 109 tf
BSU24020 109 tf
BSU31530 109 tf
BSU36020 109 tf
BSU40540 109 tf

Warning: BSU40540 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
5172 7.50e-04 aAAGgAGgtgg
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5173 5.00e+03 AGcgGgCccTtTC
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5440 9.40e+00 atAgaAAaaAAggtg
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5441 1.90e+01 aGgGGGaAtT
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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 BSU40540

BSU40540 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for BSU40540

BSU40540 has total of 42 gene neighbors in modules 109, 249
Gene neighbors (42)
Gene Common Name Description Module membership
BSU03620 yclA putative transcriptional regulator (LysR family) (RefSeq) 109, 378
BSU05270 ydzF putative transcriptional regulator (RefSeq) 109, 381
BSU08560 yfhJ hypothetical protein (RefSeq) 109, 354
BSU08900 yhzB hypothetical protein (RefSeq) 109, 354
BSU09430 citR transcriptional regulator CitR (LysR family) (RefSeq) 109, 378
BSU10410 yhzC hypothetical protein (RefSeq) 249, 381
BSU10510 yhjH putative transcriptional regulator (RefSeq) 109, 378
BSU11550 yjbH putative thiol management oxidoreductase component (RefSeq) 82, 109
BSU13700 clpE ATP-dependent Clp protease (class III stress gene) (RefSeq) 249, 379
BSU13760 ykvN putative transcriptional regulator (RefSeq) 109, 249
BSU13800 ykvR hypothetical protein (RefSeq) 109, 216
BSU13850 zosA Zn transporter (RefSeq) 111, 249
BSU21680 yppQ methionine sulfoxide reductase B (RefSeq) 249, 373
BSU21690 msrA methionine sulfoxide reductase A (RefSeq) 249, 373
BSU22580 ypiB hypothetical protein (RefSeq) 249, 340
BSU22590 ypiA hypothetical protein (RefSeq) 249, 340
BSU23520 fur transcriptional regulator for iron transport and metabolism (RefSeq) 49, 249
BSU23630 yqkE hypothetical protein (RefSeq) 109, 373
BSU24950 pstBB phosphate ABC transporter ATP-binding protein (RefSeq) 249, 349
BSU24960 pstBA phosphate ABC transporter ATP-binding protein (RefSeq) 249, 349
BSU24970 pstA phosphate ABC transporter (permease) (RefSeq) 249, 349
BSU24980 pstC phosphate ABC transporter (permease) (RefSeq) 249, 349
BSU24990 pstS phosphate ABC transporter (binding lipoprotein) (RefSeq) 249, 349
BSU25780 arsC arsenate reductase (RefSeq) 161, 249
BSU25790 arsB arsenite efflux transporter (RefSeq) 49, 249
BSU25800 yqcK putative thiol lyase (RefSeq) 49, 249
BSU25810 arsR transcriptional regulator (ArsR family) (RefSeq) 49, 249
BSU26380 yqaB conserved hypothetical protein; skin element (RefSeq) 109, 378
BSU30020 ytzE putative transcriptional regulator (DeoR family) (RefSeq) 91, 249
BSU31300 yugS putative membrane protein involved in divalent ion export (RefSeq) 109, 137
BSU31310 yugP putative metal-dependent protease/peptidase (RefSeq) 109, 259
BSU32160 yutM putative chaperone involved in Fe-S cluster assembly (RefSeq) 109, 381
BSU32780 yusF putative ribonuclease (RefSeq) 109, 354
BSU33490 copB copper(I)-transporting ATPase (RefSeq) 161, 249
BSU34480 yvdT putative transcriptional regulator (TetR/AcrR family) (RefSeq) 249, 393
BSU36080 ywrF hypothetical protein (RefSeq) 109, 412
BSU39250 yxiE phosphate starvation protein (universal stress protein A family) (RefSeq) 249, 381
BSU39790 yxcE hypothetical protein (RefSeq) 109, 373
BSU39800 yxcD hypothetical protein (RefSeq) 109, 373
BSU40540 yybR putative transcriptional regulator (RefSeq) 109, 249
BSU40760 yyaP putative oxidoreductase (RefSeq) 109, 378
VIMSS36736 VIMSS36736 None 191, 249
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 BSU40540
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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