Organism : Bacillus cereus ATCC14579 | Module List:
Module 7 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 7

There are 12 regulatory influences for Module 7

Regulator Table (12)
Regulator Name Type
BC2122 tf
BC2558 tf
BC3244 tf
BC5171 tf
BC0806 tf
BC4256 tf
BC0405 tf
BC4826 tf
BC0630 tf
BC1932 tf
BC3163 tf
BC0961 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
3936 3.90e-03 TCccCTtcTttttcT
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3937 3.90e+03 ctCACTtTAT
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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 7 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 3.14e-02 4.96e-02 5/38
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 7

There are 38 genes in Module 7

Gene Member Table (38)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0205 BC0205 CDS None chromosome 182161 182664 + hypothetical protein (NCBI ptt file) False
BC0616 BC0616 CDS None chromosome 608500 609468 - Iron(III) dicitrate-binding protein (NCBI ptt file) False
BC0630 BC0630 CDS None chromosome 625300 626010 + Trehalose operon transcriptional repressor (NCBI ptt file) True
BC0681 BC0681 CDS None chromosome 679000 679473 + hypothetical protein (NCBI ptt file) False
BC0805 BC0805 CDS None chromosome 789149 790237 + outer surface protein (NCBI ptt file) False
BC0806 BC0806 CDS None chromosome 790323 792254 + Transcription antiterminator, BglG family (NCBI ptt file) True
BC0961 BC0961 CDS None chromosome 948587 949162 - Transcriptional regulator, TetR family (NCBI ptt file) True
BC1133 BC1133 CDS None chromosome 1114162 1114347 - hypothetical protein (NCBI ptt file) False
BC1177 BC1177 DUMMY None chromosome 0 0 + None False
BC1345 BC1345 CDS None chromosome 1321523 1321708 - hypothetical protein (NCBI ptt file) False
BC1349 BC1349 CDS None chromosome 1322851 1323429 - Acetyltransferase (NCBI ptt file) False
BC1601 BC1601 CDS None chromosome 1561271 1561447 + hypothetical protein (NCBI ptt file) False
BC1962 BC1962 CDS None chromosome 1909530 1910138 - Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) False
BC2062 BC2062 CDS None chromosome 2003743 2004204 - hypothetical protein (NCBI ptt file) False
BC2516 BC2516 CDS None chromosome 2489733 2490449 - Short chain dehydrogenase (NCBI ptt file) False
BC2558 BC2558 CDS None chromosome 2533456 2533806 - Transcriptional regulator (NCBI ptt file) True
BC2585 BC2585 CDS None chromosome 2550334 2551518 + Portal protein (NCBI ptt file) False
BC2659 BC2659 CDS None chromosome 2641708 2642214 + Glutamate-rich protein grpB (NCBI ptt file) False
BC2908 BC2908 CDS None chromosome 2865168 2865989 + hypothetical protein (NCBI ptt file) False
BC2950 BC2950 CDS None chromosome 2909343 2909867 + putative kinase (NCBI ptt file) False
BC2957 BC2957 CDS None chromosome 2914369 2914719 + hypothetical protein (NCBI ptt file) False
BC2995 BC2995 CDS None chromosome 2953123 2953659 - hypothetical protein (NCBI ptt file) False
BC2996 BC2996 CDS None chromosome 2953667 2953984 - Transcriptional regulator, PadR family (NCBI ptt file) True
BC3279 BC3279 CDS None chromosome 3255886 3256269 + hypothetical protein (NCBI ptt file) False
BC3318 BC3318 CDS None chromosome 3284531 3284842 + hypothetical protein (NCBI ptt file) False
BC3331 BC3331 CDS None chromosome 3295014 3295373 + hypothetical protein (NCBI ptt file) False
BC3333 BC3333 CDS None chromosome 3295640 3296605 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC3411 BC3411 CDS None chromosome 3374032 3374454 + XoxI (NCBI ptt file) False
BC3448 BC3448 CDS None chromosome 3406770 3407123 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC3536 BC3536 CDS None chromosome 3504399 3504746 - hypothetical protein (NCBI ptt file) False
BC3606 BC3606 CDS None chromosome 3583138 3583557 - Esterase (NCBI ptt file) False
BC4241 BC4241 CDS None chromosome 4188413 4188655 + hypothetical protein (NCBI ptt file) False
BC4532 BC4532 CDS None chromosome 4478216 4478548 + hypothetical protein (NCBI ptt file) False
BC4675 BC4675 CDS None chromosome 4614442 4615464 - Sex pheromone staph-cAM373 precursor (NCBI ptt file) False
BC5170 BC5170 CDS None chromosome 5069156 5069776 - Integral membrane protein (NCBI ptt file) False
BC5171 BC5171 CDS None chromosome 5069773 5070537 - Transcriptional regulator, MerR family (NCBI ptt file) True
BC5187 BC5187 CDS None chromosome 5085085 5085396 - Cytochrome c551 (NCBI ptt file) False
BC5490 BC5490 CDS None chromosome 5411393 5411527 - LSU ribosomal protein L34P (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.

Comments for Module 7

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.