Organism : Bacillus subtilis | Module List :
BSU40170 yydG

putative AdoMet radical enzyme (RefSeq)

CircVis
Functional Annotations (4)
Function System
Predicted Fe-S oxidoreductases cog/ cog
catalytic activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
rSAM_yydG tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU40170
(Mouseover regulator name to see its description)

BSU40170 is regulated by 25 influences and regulates 0 modules.
Regulators for BSU40170 yydG (25)
Regulator Module Operator
BSU00370 306 tf
BSU11930 306 tf
BSU26220 306 tf
BSU26870 306 tf
BSU27080 306 tf
BSU27320 306 tf
BSU30150 306 tf
BSU34380 306 tf
BSU36420 306 tf
BSU37290 306 tf
BSU40050 306 tf
BSU40410 306 tf
BSU40710 306 tf
BSU01730 162 tf
BSU01740 162 tf
BSU09480 162 tf
BSU09560 162 tf
BSU19050 162 tf
BSU23100 162 tf
BSU24220 162 tf
BSU25250 162 tf
BSU34220 162 tf
BSU37080 162 tf
BSU40050 162 tf
BSU40410 162 tf

Warning: BSU40170 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
5272 1.40e-02 AGGAGG
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5273 1.60e-01 AAAAaTgAaacttTT
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5550 2.00e-01 ccCTCCttTac
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5551 2.30e+04 GCCGTC
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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 BSU40170

BSU40170 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted Fe-S oxidoreductases cog/ cog
catalytic activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
rSAM_yydG tigr/ tigrfam
Module neighborhood information for BSU40170

BSU40170 has total of 53 gene neighbors in modules 162, 306
Gene neighbors (53)
Gene Common Name Description Module membership
BSU02310 ybfO putative exported hydrolase (RefSeq) 306, 329
BSU02700 estA secreted alkaliphilic lipase (RefSeq) 162, 313
BSU04590 ydbS hypothetical protein (RefSeq) 92, 162
BSU04600 ydbT hypothetical protein (RefSeq) 92, 162
BSU06180 pspA phage shock protein A homolog (RefSeq) 7, 162
BSU06190 ydjG putative phage replication protein (RefSeq) 162, 313
BSU06200 ydjH hypothetical protein (RefSeq) 162, 313
BSU06210 ydjI hypothetical protein (RefSeq) 162, 312
BSU12460 xlyB N-acetylmuramoyl-L-alanine amidase; bacteriophage PBSX protein (RefSeq) 239, 306
BSU14340 yknW putative permease (RefSeq) 92, 162
BSU14350 yknX putative efflux permease (RefSeq) 162, 313
BSU14360 yknY putative ABC transporter (ATP-binding protein) (RefSeq) 92, 162
BSU14370 yknZ putative permease (RefSeq) 92, 162
BSU15300 bpr bacillopeptidase F (RefSeq) 12, 306
BSU17120 pksE enzyme involved in polyketide synthesis (RefSeq) 85, 306
BSU17130 acpK acyl carrier protein (RefSeq) 85, 306
BSU17140 pksF polyketide beta-ketoacyl:acyl carrier protein synthase (RefSeq) 85, 306
BSU17150 pksG acetyl-S-AcpK beta-ketothioester polyketide intermediate transferase (RefSeq) 85, 306
BSU17160 pksH polyketide biosynthesis enoyl-CoA hydratase (RefSeq) 85, 306
BSU17170 pksI polyketide biosynthesis enoyl-CoA hydratase (RefSeq) 85, 306
BSU17180 pksJ polyketide synthase of type I (RefSeq) 85, 306
BSU17190 pksL polyketide synthase of type I (RefSeq) 85, 306
BSU17200 pksM polyketide synthase (RefSeq) 85, 306
BSU17210 pksN polyketide synthase of type I (RefSeq) 85, 306
BSU17220 pksR polyketide synthase (RefSeq) 85, 306
BSU18310 ppsD plipastatin synthetase (RefSeq) 98, 306
BSU18320 ppsC plipastatin synthetase (RefSeq) 306, 335
BSU18330 ppsB plipastatin synthetase (RefSeq) 85, 306
BSU18340 ppsA plipastatin synthetase (RefSeq) 85, 306
BSU18590 yoaG putative permease (RefSeq) 162, 166
BSU21440 bdbB bacteriophage SPbeta thiol-disulfide oxidoreductase (RefSeq) 298, 306
BSU21450 yolJ putative glycosyltransferase (RefSeq) 298, 306
BSU21460 bdbA bacteriophage SPbeta thiol-disulfide oxidoreductase (RefSeq) 298, 306
BSU21470 sunT sublancin 168 lantibiotic transporter (RefSeq) 298, 306
BSU23480 dacF D-alanyl-D-alanine carboxypeptidase (penicilin binding protein) (RefSeq) 126, 306
BSU25360 yqfC hypothetical protein (RefSeq) 162, 280
BSU25370 yqfB hypothetical protein (RefSeq) 162, 166
BSU25380 yqfA hypothetical protein (RefSeq) 162, 166
BSU25390 yqeZ putative membrane bound hydrolase (RefSeq) 162, 166
BSU28240 ysoA putative hydrolase (RefSeq) 162, 193
BSU29520 yteJ putative integral inner membrane protein (RefSeq) 92, 162
BSU29530 sppA signal peptide peptidase (RefSeq) 92, 162
BSU33750 sdpA export of killing factor (RefSeq) 162, 306
BSU33760 sdpB exporter of killing factor SpbC (RefSeq) 162, 306
BSU33770 spbC killing factor SdpC (RefSeq) 162, 344
BSU40160 yydH putative membrane metalloprotease (RefSeq) 36, 306
BSU40170 yydG putative AdoMet radical enzyme (RefSeq) 162, 306
BSU40580 yybN hypothetical protein (RefSeq) 36, 162
BSU40590 yybM putative integral inner membrane protein (RefSeq) 36, 162
BSU40600 yybL putative integral inner membrane protein (RefSeq) 162, 313
BSU40610 yybK putative integral inner membrane protein (RefSeq) 162, 313
BSU40620 yybJ putative ATP-binding cassette protein (RefSeq) 162, 313
VIMSS36968 VIMSS36968 None 162, 184
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 BSU40170
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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