Organism : Bacillus subtilis | Module List :
BSU11500 spxA

transcriptional regulator Spx (RefSeq)

CircVis
Functional Annotations (7)
Function System
Arsenate reductase and related proteins, glutaredoxin family cog/ cog
electron transport go/ biological_process
arsenate reductase (glutaredoxin) activity go/ molecular_function
electron carrier activity go/ molecular_function
protein disulfide oxidoreductase activity go/ molecular_function
oxidoreductase activity go/ molecular_function
arsC_related tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU11500
(Mouseover regulator name to see its description)

BSU11500 is regulated by 23 influences and regulates 9 modules.
Regulators for BSU11500 spxA (23)
Regulator Module Operator
BSU01730 77 tf
BSU04680 77 tf
BSU05270 77 tf
BSU08370 77 tf
BSU11500 77 tf
BSU15640 77 tf
BSU19090 77 tf
BSU19120 77 tf
BSU23100 77 tf
BSU27110 77 tf
BSU27320 77 tf
BSU28820 77 tf
BSU29270 77 tf
BSU34060 77 tf
BSU36020 77 tf
BSU40050 77 tf
BSU40540 77 tf
BSU00830 388 tf
BSU02890 388 tf
BSU04730 388 tf
BSU06960 388 tf
BSU25490 388 tf
BSU36020 388 tf

Warning: BSU11500 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
5108 2.20e+01 aGGAagaG
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5109 1.40e+02 GGcctGCCcgC
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5688 5.20e+03 ctgtaAAggAGGtG
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5689 8.60e+03 GcAAaTTcTttaGAA
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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 BSU11500

BSU11500 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Arsenate reductase and related proteins, glutaredoxin family cog/ cog
electron transport go/ biological_process
arsenate reductase (glutaredoxin) activity go/ molecular_function
electron carrier activity go/ molecular_function
protein disulfide oxidoreductase activity go/ molecular_function
oxidoreductase activity go/ molecular_function
arsC_related tigr/ tigrfam
Module neighborhood information for BSU11500

BSU11500 has total of 41 gene neighbors in modules 77, 388
Gene neighbors (41)
Gene Common Name Description Module membership
BSU00830 ctsR transcriptional regulator (RefSeq) 68, 388
BSU00840 mcsA activator of protein kinase McsB (RefSeq) 68, 388
BSU00850 mcsB ATP:guanido phosphotransferase (RefSeq) 68, 388
BSU00860 clpC class III stress response-related ATPase, AAA+ superfamily (RefSeq) 68, 388
BSU00870 radA DNA repair protein RadA (RefSeq) 68, 388
BSU00880 yacK DNA integrity scanning protein DisA (RefSeq) 68, 388
BSU00890 yacL hypothetical protein (RefSeq) 54, 388
BSU00900 ispD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (RefSeq) 70, 388
BSU02880 yceB putative monooxygenase (RefSeq) 77, 259
BSU02890 yceC putative stress adaptation protein (RefSeq) 324, 388
BSU02900 yceD putative stress adaptation protein (RefSeq) 324, 388
BSU02910 yceE putative stress adaptation protein (RefSeq) 324, 388
BSU02920 yceF putative stress adaptation transporter (RefSeq) 324, 388
BSU02930 yceG hypothetical protein (RefSeq) 324, 388
BSU02940 yceH hypothetical protein (RefSeq) 324, 388
BSU03860 ycnD NADPH-FMN oxidoreductase (nitroreductase) (RefSeq) 68, 77
BSU03870 ycnE hypothetical protein (RefSeq) 68, 77
BSU07990 yfjR putative beta-hydroxyacid dehydrogenase (RefSeq) 77, 259
BSU11500 spxA transcriptional regulator Spx (RefSeq) 77, 388
BSU12410 yjoA hypothetical protein (RefSeq) 77, 259
BSU13030 ykhA putative acyl-CoA hydrolase (RefSeq) 77, 82
BSU23820 yqjM NADPH dehydrogenase NamA (RefSeq) 77, 259
BSU24180 yqiK putative glycerophosphodiester phosphodiesterase (RefSeq) 77, 259
BSU25470 dnaK molecular chaperone DnaK (RefSeq) 68, 388
BSU25480 grpE heat shock protein GrpE (RefSeq) 68, 388
BSU25490 hrcA heat-inducible transcription repressor (RefSeq) 68, 388
BSU27820 yrbC hypothetical protein (RefSeq) 77, 259
BSU28190 engB ribosome biogenesis GTP-binding protein YsxC (RefSeq) 77, 259
BSU28500 trxA thioredoxin (RefSeq) 77, 259
BSU29540 ppnK inorganic polyphosphate/ATP-NAD kinase (RefSeq) 77, 359
BSU30580 ytmA putative hydrolase (RefSeq) 77, 412
BSU31360 yugK putative NADH-dependent butanol dehydrogenase (RefSeq) 77, 259
BSU31370 yugJ putative NADH-dependent butanol dehydrogenase (RefSeq) 77, 259
BSU32790 yusG hypothetical protein (RefSeq) 77, 78
BSU33190 yvrD putative oxidoreductase (RefSeq) 77, 259
BSU33950 cggR transcriptional regulator of gapA (RefSeq) 237, 388
BSU35300 secA preprotein translocase subunit SecA (RefSeq) 237, 388
BSU35990 ywrO nitroreductase (RefSeq) 77, 259
BSU36910 ywlG hypothetical protein (RefSeq) 77, 160
BSU36920 ywlF ribose-5-phosphate isomerase B (RefSeq) 77, 160
BSU38370 ywbC putative lyase (RefSeq) 77, 78
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 BSU11500
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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