Organism : Bacillus subtilis | Module List:
Module 318 Profile

GeneModule member RegulatorRegulator MotifMotif
Cytoscape Web
Network Help

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges.

Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif
Regulators for Module 318

There are 16 regulatory influences for Module 318

Regulator Table (16)
Regulator Name Type
BSU33580 tf
BSU34060 tf
BSU26320 tf
BSU10880 tf
BSU34630 tf
BSU01430 tf
BSU03560 tf
BSU07590 tf
BSU40130 tf
BSU23090 tf
BSU39430 tf
BSU05370 tf
BSU07010 tf
BSU02550 tf
BSU34180 tf
BSU08370 tf

Regulator Help

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type.

tf: Transcription factor

ef: Environmental factor

combiner: Combinatorial influence of a tf or an ef through logic gate. Table is sortable by clicking on the arrows next to column headers.

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
5574 2.90e-03 aaGgggGg
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5575 1.50e+03 CGgagTGAGAA
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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

Regulon 318 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 6.37e-03 1.69e-02 5/31
Glycolysis / Gluconeogenesis kegg pathway 2.17e-04 1.74e-03 3/31
Pentose and glucuronate interconversions kegg pathway 5.40e-05 6.09e-04 3/31
Environmental Information Processing kegg category 1.51e-02 3.15e-02 5/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 2.24e-02 3.44e-02 8/31
Transcription cog subcategory 8.49e-04 1.57e-03 7/31
Signal transduction mechanisms cog subcategory 9.51e-04 1.75e-03 5/31
Carbohydrate transport and metabolism cog subcategory 1.61e-02 2.53e-02 5/31
Functions Help

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

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.

Members for Module 318

There are 31 genes in Module 318

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU02440 glnJ CDS None chromosome 265536 266699 + two-component sensor histidine kinase [GlnL] for glutamine degradation (RefSeq) False
BSU03560 ycxD CDS None chromosome 405703 407037 + putative PLP-dependent transcriptional regulator (RefSeq) True
BSU08380 yfiS CDS None chromosome 911882 913135 - putative efflux transporter (RefSeq) False
BSU09320 yhcY CDS None chromosome 1007953 1009092 + two-component sensor histidine kinase [YhcZ] (RefSeq) False
BSU09330 yhcZ CDS None chromosome 1009089 1009733 + two-component response regulator [YhcY] (RefSeq) True
BSU09490 yhdJ CDS None chromosome 1027082 1027510 + putative acetyltransferase (RefSeq) False
BSU10880 yisV CDS None chromosome 1166042 1167496 + putative PLP-dependent transcriptional regulator (RefSeq) True
BSU12380 uxaB CDS None chromosome 1309190 1310632 + altronate oxidoreductase (RefSeq) False
BSU12390 uxaA CDS None chromosome 1310629 1312122 + altronate hydrolase (RefSeq) False
BSU26180 yqbA CDS None chromosome 2685996 2687528 - putative phage capsid protein; skin element (RefSeq) False
BSU32440 pucK CDS None chromosome 3330883 3332175 + uric acid permease (RefSeq) False
BSU32520 pucG CDS None chromosome 3340193 3341443 - putative ureidoglycolate lyase (ureidoglycolase) (RefSeq) False
BSU32530 yurH CDS None chromosome 3341460 3342698 - allantoate amidohydrolase (RefSeq) False
BSU33560 yvaD CDS None chromosome 3447325 3447726 - putative integral inner membrane protein (RefSeq) False
BSU33570 yvaE CDS None chromosome 3447723 3448082 - putative metabolite-efflux transporter (RefSeq) False
BSU33580 yvaF CDS None chromosome 3448079 3448651 - putative transcriptional regulator (RefSeq) True
BSU34060 yvfU CDS None chromosome 3494907 3495509 - two-component response regulator [YvfT] (RefSeq) True
BSU34070 yvfT CDS None chromosome 3495526 3496512 - two-component sensor histidine kinase [YvfU] (RefSeq) False
BSU34080 yvfS CDS None chromosome 3496645 3497382 - putative ABC transporter (permease) (RefSeq) False
BSU34090 yvfR CDS None chromosome 3497383 3498288 - putative ABC efflux transporter (ATP-binding protein) (RefSeq) False
BSU34630 mdxR CDS None chromosome 3556814 3557764 - putative transcriptional regulator (LacI family) (RefSeq) True
BSU35880 pgsA CDS None chromosome 3696848 3697990 - capsular polyglutamate synthetase (RefSeq) False
BSU36320 ywpG CDS None chromosome 3739651 3740034 - hypothetical protein (RefSeq) False
BSU36340 ywpE CDS None chromosome 3740758 3741066 - putative sortase (RefSeq) False
BSU38640 yxlH CDS None chromosome 3965765 3966967 + putative efflux transporter (RefSeq) False
BSU39860 aldX CDS None chromosome 4093000 4094337 + putative aldehyde dehydrogenase (RefSeq) False
BSU40110 bglA CDS None chromosome 4120190 4121629 - aryl-6-phospho-beta-glucosidase (RefSeq) False
BSU40120 yyzE CDS None chromosome 4121643 4121873 - putative phosphotransferase system enzyme IIA component (RefSeq) False
BSU40130 yydK CDS None chromosome 4122217 4122927 + putative transcriptional regulator (GntR family) (RefSeq) True
BSU40260 yycQ CDS None chromosome 4136387 4136635 - putative conserved membrane protein (RefSeq) False
BSU40700 yybB CDS None chromosome 4181660 4182322 - putative hydrolase (RefSeq) False

Genes Help

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Comments for Module 318

Please add your comments for this module by using the form below. Your comments will be publicly available.

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Social Help

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Module Overview

The landing module page shows quick summary info including co-expression profiles, de-novo identified motifs, and transcription factors and/or environmental factors as regulatory influences. It also includes module residual, motif e-values, conditions and links to other resources such as NCBI and Microbesonline. . If a transcription factor is included in the manually curated RegPrecise database, further information from RegPrecise is shown, allowing users to perform comparative analysis.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Network

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges. Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

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.

Functions

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

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.

Genes

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Social

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Definitions

Residual: is a measure of bicluster quality. Mean bicluster residual is smaller when the expression profile of the genes in the module is "tighter". So smaller residuals are usually indicative of better bicluster quality.

Expression Profile: is a preview of the expression profiles of all the genes under subset of conditions included in the module. Tighter expression profiles are usually indicative of better bicluster quality.

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.

Genes: Number of genes included in the module.

Functions: We identify functional enrichment of each module by camparing to different functional categories such as KEGG, COG, GO etc. by using hypergeometric function. If the module is significantly enriched for any of the functions, this column will list few of the these functions as an overview. Full list of functions is available upon visiting the module page under the Functions tab.