Organism : Bacillus subtilis | Module List:
Module 231 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 231

There are 14 regulatory influences for Module 231

Regulator Table (14)
Regulator Name Type
BSU40350 tf
BSU09480 tf
BSU00800 tf
BSU26220 tf
BSU07010 tf
BSU14740 tf
BSU26320 tf
BSU18460 tf
BSU39850 tf
BSU32870 tf
BSU28410 tf
BSU35490 tf
BSU02160 tf
BSU37290 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
5406 1.10e+03 aCAGcCGaatCGcgCaG
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5407 1.10e+02 GcaAatatcgaaaGGagaAtG
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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 231 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.35e-04 1.21e-03 13/29
Carbohydrate Metabolism kegg subcategory 1.27e-04 1.16e-03 7/29
Butanoate metabolism kegg pathway 4.10e-05 4.89e-04 3/29
Nucleotide Metabolism kegg subcategory 4.70e-05 5.46e-04 5/29
Purine metabolism kegg pathway 7.00e-06 1.15e-04 5/29
Global kegg category 1.91e-03 8.08e-03 10/29
Metabolism kegg subcategory 1.91e-03 8.08e-03 10/29
Metabolic pathways kegg pathway 1.10e-03 5.64e-03 10/29
Microbial metabolism in diverse environments kegg pathway 1.34e-04 1.20e-03 6/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 3.21e-02 4.83e-02 13/29
Lipid transport and metabolism cog subcategory 7.01e-03 1.15e-02 3/29
General function prediction only cog subcategory 4.70e-03 7.85e-03 7/29
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 231

There are 29 genes in Module 231

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU01590 ybaS CDS None chromosome 178733 179584 + putative sodium dependent transporter (RefSeq) False
BSU02110 ybyB CDS None chromosome 230807 231067 - hypothetical protein (RefSeq) False
BSU03690 yczF CDS None chromosome 419331 419552 - hypothetical protein (RefSeq) False
BSU03900 gabT CDS None chromosome 441139 442449 + 4-aminobutyrate aminotransferase (RefSeq) False
BSU06170 ydjE CDS None chromosome 669635 670597 + putative sugar kinase (ribokinase family) (RefSeq) False
BSU12490 yjqC CDS None chromosome 1319001 1319837 + putative PBSX phage manganese-containing catalase (RefSeq) False
BSU13190 ispA CDS None chromosome 1385330 1386289 - intracellular serine protease (RefSeq) False
BSU14410 sipT CDS None chromosome 1510615 1511196 + type I signal peptidase (RefSeq) False
BSU14720 ylaB CDS None chromosome 1543123 1543392 + hypothetical protein (RefSeq) False
BSU14740 ylaD CDS None chromosome 1543910 1544203 + anti-YlaC sigma factor (RefSeq) True
BSU19800 phy CDS None chromosome 2149306 2150454 - phytase (RefSeq) False
BSU23080 aroD CDS None chromosome 2411900 2412667 - 3-dehydroquinate dehydratase (RefSeq) False
BSU25730 yqeC CDS None chromosome 2649710 2650603 - 6-phosphogluconate dehydrogenase-like protein (RefSeq) False
BSU27080 levR CDS None chromosome 2762250 2765066 - transcriptional regulator (NifA/NtrC family) (RefSeq) True
BSU27420 yrrI CDS None chromosome 2800368 2801429 - putative permease (RefSeq) False
BSU30250 ytaP CDS None chromosome 3094714 3095613 - putative hydrolase (RefSeq) False
BSU32230 yuxL CDS None chromosome 3309789 3311762 - putative acylaminoacyl-peptidase (RefSeq) False
BSU32410 pucH CDS None chromosome 3326273 3327613 - allantoinase (RefSeq) False
BSU32450 pucL CDS None chromosome 3332188 3333672 + urate oxidase with peroxide reductase N-terminal domain (RefSeq) False
BSU32460 pucM CDS None chromosome 3333651 3334016 + urate oxidase structural factor (RefSeq) False
BSU32500 pucB CDS None chromosome 3338382 3338975 - enzyme for molybdopterin cofactor synthesis required for xanthine dehydrogenase (RefSeq) False
BSU32510 pucA CDS None chromosome 3338972 3339964 - xanthine dehydrogenase molybdopterin recruitment factor (RefSeq) False
BSU34460 levB CDS None chromosome 3536537 3538087 + endolevanase (RefSeq) False
BSU38790 yxzE CDS None chromosome 3981992 3982192 + putative bacteriocin (RefSeq) False
BSU38970 yxjF CDS None chromosome 3999557 4000330 - 3-hydroxybutyrate dehydrogenase (RefSeq) False
BSU38980 scoB CDS None chromosome 4000347 4000997 - succinyl CoA:3-oxoacid CoA-transferase (subunit B) (RefSeq) False
BSU40430 yycE CDS None chromosome 4155955 4156374 - hypothetical protein (RefSeq) False
BSU40570 yybO CDS None chromosome 4169069 4170376 + putative permease (RefSeq) False
BSU40740 yyaR CDS None chromosome 4184184 4184705 - putative acetyl-transferase (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 231

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.