Organism : Bacillus cereus ATCC14579 | Module List:
Module 467 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 467

There are 14 regulatory influences for Module 467

Regulator Table (14)
Regulator Name Type
BC0114 tf
BC3253 tf
BC4316 tf
BC3313 tf
BC1302 tf
BC3332 tf
BC4374 tf
BC0213 tf
BC0073 tf
BC1814 tf
BC0057 tf
BC2794 tf
BC3062 tf
BC3653 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
4844 1.40e+00 cgtacGaAAGg
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4845 7.40e+02 AggggAGggAc
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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 467 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Cofactors and Vitamins kegg subcategory 2.81e-04 2.49e-03 4/25
Ubiquinone and other terpenoid-quinone biosynthesis kegg pathway 0.00e+00 0.00e+00 4/25
Environmental Information Processing kegg category 3.00e-06 8.50e-05 8/25
Membrane Transport kegg subcategory 0.00e+00 7.00e-06 8/25
ABC transporters kegg pathway 0.00e+00 2.00e-06 8/25
Biosynthesis of secondary metabolites kegg pathway 1.28e-02 2.87e-02 4/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 7.20e-05 1.57e-04 4/25
Menaquinone and ubiquinone tigr sub1role 0.00e+00 0.00e+00 4/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 3.34e-03 6.13e-03 12/25
Inorganic ion transport and metabolism cog subcategory 0.00e+00 2.00e-06 8/25
General function prediction only cog subcategory 2.21e-02 3.60e-02 5/25
ABC-type Fe3+-siderophore transport system, permease component cog 0.00e+00 0.00e+00 5/25
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 467

There are 25 genes in Module 467

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0381 BC0381 CDS None chromosome 363215 364222 - Ferrichrome transport system permease protein fhuG (NCBI ptt file) False
BC0382 BC0382 CDS None chromosome 364219 365235 - Ferrichrome transport system permease protein fhuB (NCBI ptt file) False
BC0383 BC0383 CDS None chromosome 365308 366228 - Ferrichrome-binding protein (NCBI ptt file) False
BC0424 BC0424 CDS None chromosome 414088 414408 + IG hypothetical 16092 (NCBI ptt file) False
BC0425 BC0425 CDS None chromosome 414386 415153 + Hydroxymethylpyrimidine transport system permease protein (NCBI ptt file) False
BC0426 BC0426 CDS None chromosome 415150 416148 + Hydroxymethylpyrimidine-binding protein (NCBI ptt file) False
BC0513 BC0513 CDS None chromosome 504271 505284 + Daunorubicin resistance ATP-binding protein drrA (NCBI ptt file) False
BC0514 BC0514 CDS None chromosome 505277 506068 + Daunorubicin resistance transmembrane protein (NCBI ptt file) False
BC0515 BC0515 CDS None chromosome 506073 506858 + ABC transporter permease protein (NCBI ptt file) False
BC0516 BC0516 CDS None chromosome 506931 507335 + LCTB protein (NCBI ptt file) False
BC0618 BC0618 CDS None chromosome 610718 611701 + Iron(III) dicitrate transport system permease protein fecD (NCBI ptt file) False
BC1306 BC1306 CDS None chromosome 1285839 1286561 + ComC protein (NCBI ptt file) False
BC1739 BC1739 CDS None chromosome 1684575 1685846 + Proton/sodium-glutamate symport protein (NCBI ptt file) False
BC1804 BC1804 CDS None chromosome 1758444 1759403 + Rhodanese-related sulfurtransferases (NCBI ptt file) False
BC3202 BC3202 CDS None chromosome 3177556 3177771 - hypothetical protein (NCBI ptt file) False
BC3865 BC3865 CDS None chromosome 3844322 3844792 - Polypeptide deformylase (NCBI ptt file) False
BC3866 BC3866 CDS None chromosome 3844804 3847209 - Primosomal protein N' (NCBI ptt file) False
BC4309 BC4309 CDS None chromosome 4250864 4251601 - surface protein (NCBI ptt file) False
BC4851 BC4851 CDS None chromosome 4774684 4776132 - O-succinylbenzoic acid--CoA ligase (NCBI ptt file) False
BC4854 BC4854 CDS None chromosome 4777462 4778274 - Menaquinone biosynthesis related protein (NCBI ptt file) False
BC4855 BC4855 CDS None chromosome 4778271 4780025 - 2-oxoglutarate decarboxylase (NCBI ptt file) False
BC4856 BC4856 CDS None chromosome 4780022 4781416 - Isochorismate synthase (NCBI ptt file) False
BC5182 BC5182 CDS None chromosome 5078394 5080109 - Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) False
BC5382 BC5382 CDS None chromosome 5298927 5299943 - Ferrichrome transport system permease protein fhuG (NCBI ptt file) False
BC5383 BC5383 CDS None chromosome 5299940 5300995 - Ferrichrome transport system permease protein fhuB (NCBI ptt file) 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.