Organism : Bacillus subtilis | Module List:
Module 405 Profile

GeneModule member RegulatorRegulator MotifMotif
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 405

There are 8 regulatory influences for Module 405

Regulator Table (8)
Regulator Name Type
BSU37290 tf
BSU26320 tf
BSU27320 tf
BSU02220 tf
BSU05850 tf
BSU30150 tf
BSU09480 tf
BSU06960 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
5718 6.90e+00 aAAGGa.AaaG
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5719 3.40e+01 ACAtGtcTTTtcCAgaAAAaAatG
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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 405 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 2.71e-04 2.06e-03 11/24
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 8/24
Nitrogen metabolism kegg pathway 0.00e+00 0.00e+00 8/24
Environmental Information Processing kegg category 7.14e-04 4.13e-03 6/24
Signal Transduction kegg subcategory 2.00e-06 3.60e-05 6/24
Two-component system kegg pathway 2.00e-06 3.60e-05 6/24
Global kegg category 5.00e-05 5.72e-04 11/24
Metabolism kegg subcategory 5.00e-05 5.72e-04 11/24
Microbial metabolism in diverse environments kegg pathway 0.00e+00 0.00e+00 10/24

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Central intermediary metabolism tigr mainrole 1.60e-05 4.20e-05 3/24
Nitrogen metabolism tigr sub1role 0.00e+00 0.00e+00 3/24
Energy metabolism tigr mainrole 3.90e-05 8.60e-05 5/24
Anaerobic tigr sub1role 0.00e+00 0.00e+00 3/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.56e-04 5.30e-04 15/24
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 9/24
Inorganic ion transport and metabolism cog subcategory 1.84e-02 2.87e-02 3/24
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 405

There are 24 genes in Module 405

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU01890 ybcL CDS None chromosome 211845 213017 + putative efflux transporter (RefSeq) False
BSU03290 nasE CDS None chromosome 354972 355292 - assimilatory nitrite reductase subunit (RefSeq) False
BSU03300 nasD CDS None chromosome 355324 357741 - assimilatory nitrite reductase subunit (RefSeq) False
BSU03310 nasC CDS None chromosome 357863 359995 - assimilatory nitrate reductase (catalytic subunit) (RefSeq) False
BSU03320 nasB CDS None chromosome 360002 362314 - assimilatory nitrate reductase (electron transfer subunit) (RefSeq) False
BSU03330 nasA CDS None chromosome 362494 363759 + nitrate transporter (RefSeq) False
BSU03730 yclH CDS None chromosome 423776 424456 - putative ABC transporter (ATPase component) (RefSeq) False
BSU10230 yhfH CDS None chromosome 1097424 1097564 - hypothetical protein (RefSeq) False
BSU17570 xynP CDS None chromosome 1886560 1887951 + putative H+-xyloside symporter (RefSeq) False
BSU17610 xylB CDS None chromosome 1892604 1894103 + xylulose kinase (RefSeq) False
BSU18270 ynzE CDS None chromosome 1956660 1956965 - hypothetical protein (RefSeq) False
BSU20210 yorY CDS None chromosome 2169507 2169689 - hypothetical protein; phage SPbeta (RefSeq) False
BSU27010 adhA CDS None chromosome 2755537 2756586 + putative dehydrogenase (RefSeq) False
BSU28680 glcD CDS None chromosome 2932253 2933665 + glycolate oxidase subunit (RefSeq) False
BSU28690 glcF CDS None chromosome 2933662 2934996 + glycolate oxidase iron-sulfur subunit (RefSeq) False
BSU28900 ysbB CDS None chromosome 2953533 2954228 - antiholin-like protein LrgB (RefSeq) False
BSU28910 ysbA CDS None chromosome 2954250 2954690 - murein hydrolase regulator LrgA (RefSeq) False
BSU37250 narI CDS None chromosome 3822581 3823252 - nitrate reductase (gamma subunit) (RefSeq) False
BSU37260 narJ CDS None chromosome 3823249 3823803 - nitrate reductase (protein J) (RefSeq) False
BSU37270 narH CDS None chromosome 3823829 3825292 - nitrate reductase (beta subunit) (RefSeq) False
BSU37280 narG CDS None chromosome 3825282 3828968 - nitrate reductase (alpha subunit) (RefSeq) False
BSU37290 arfM CDS None chromosome 3829164 3829640 - transcriptional regulator (RefSeq) True
BSU37320 narK CDS None chromosome 3831350 3832537 - nitrite extrusion permease (RefSeq) False
BSU37430 albG CDS None chromosome 3841317 3842018 + putative integral inner membrane protein involved in subtilosin production and immunity (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.

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.