Organism : Bacillus subtilis | Module List:
Module 192 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 192

There are 11 regulatory influences for Module 192

Regulator Table (11)
Regulator Name Type
BSU33840 tf
BSU19050 tf
BSU11660 tf
BSU06580 tf
BSU09060 tf
BSU06540 tf
BSU26430 tf
BSU29030 tf
BSU08730 tf
BSU36420 tf
BSU04060 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
5330 4.50e+01 gctaaTTTaggtGcgAAagGCT
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5331 1.40e+03 GaAAGGggGAG
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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 192 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 0.00e+00 0.00e+00 17/18
Carbohydrate Metabolism kegg subcategory 2.90e-05 3.63e-04 6/18
C5-Branched dibasic acid metabolism kegg pathway 0.00e+00 0.00e+00 4/18
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 10/18
Glycine serine and threonine metabolism kegg pathway 6.00e-06 9.10e-05 3/18
Valine leucine and isoleucine biosynthesis kegg pathway 0.00e+00 0.00e+00 7/18
Metabolism of Cofactors and Vitamins kegg subcategory 0.00e+00 0.00e+00 9/18
Pantothenate and CoA biosynthesis kegg pathway 1.00e-06 1.50e-05 3/18
Biotin metabolism kegg pathway 0.00e+00 0.00e+00 5/18
Global kegg category 0.00e+00 0.00e+00 17/18
Metabolism kegg subcategory 0.00e+00 0.00e+00 17/18
Metabolic pathways kegg pathway 0.00e+00 0.00e+00 17/18
Biosynthesis of secondary metabolites kegg pathway 0.00e+00 1.00e-06 9/18
Microbial metabolism in diverse environments kegg pathway 5.70e-05 6.33e-04 5/18

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid biosynthesis tigr mainrole 0.00e+00 0.00e+00 9/18
Pyruvate family tigr sub1role 0.00e+00 0.00e+00 7/18
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 1.00e-06 4.00e-06 5/18
Biotin tigr sub1role 0.00e+00 0.00e+00 5/18

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 0.00e+00 0.00e+00 17/18
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 10/18
Coenzyme transport and metabolism cog subcategory 0.00e+00 0.00e+00 7/18
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 192

There are 18 genes in Module 192

Gene Member Table (18)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU14860 pycA CDS None chromosome 1553492 1556938 + pyruvate carboxylase (RefSeq) False
BSU28250 leuD CDS None chromosome 2888005 2888604 - isopropylmalate isomerase small subunit (RefSeq) False
BSU28260 leuC CDS None chromosome 2888617 2890035 - isopropylmalate isomerase large subunit (RefSeq) False
BSU28270 leuB CDS None chromosome 2890085 2891182 - 3-isopropylmalate dehydrogenase (RefSeq) False
BSU28280 leuA CDS None chromosome 2891203 2892759 - 2-isopropylmalate synthase (RefSeq) False
BSU28290 ilvC CDS None chromosome 2892746 2893774 - ketol-acid reductoisomerase (RefSeq) False
BSU28300 ilvH CDS None chromosome 2893791 2894315 - acetolactate synthase 3 regulatory subunit (RefSeq) False
BSU28310 ilvB CDS None chromosome 2894312 2896036 - acetolactate synthase catalytic subunit (RefSeq) False
BSU30180 ytbQ CDS None chromosome 3087437 3088042 - putative nucleoside-diphosphate-sugar epimerase (RefSeq) False
BSU30190 bioI CDS None chromosome 3088275 3089462 - cytochrome P450 for pimelic acid formation for biotin biosynthesis (RefSeq) False
BSU30200 bioB CDS None chromosome 3089531 3090538 - biotin synthase (RefSeq) False
BSU30210 bioD CDS None chromosome 3090541 3091236 - dithiobiotin synthetase (RefSeq) False
BSU30220 bioF CDS None chromosome 3091233 3092402 - 8-amino-7-oxononanoate synthase (RefSeq) False
BSU30230 bioA CDS None chromosome 3092392 3093738 - adenosylmethionine--8-amino-7-oxononanoate transaminase (RefSeq) False
BSU30240 bioW CDS None chromosome 3093728 3094507 - 6-carboxyhexanoate--CoA ligase (RefSeq) False
BSU32240 thrB CDS None chromosome 3311870 3312799 - homoserine kinase (RefSeq) False
BSU32250 thrC CDS None chromosome 3312796 3313854 - threonine synthase (RefSeq) False
BSU32260 hom CDS None chromosome 3313854 3315155 - homoserine dehydrogenase (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 192

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.