Organism : Bacillus cereus ATCC14579 | Module List:
Module 72 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 72

There are 6 regulatory influences for Module 72

Regulator Table (6)
Regulator Name Type
BC2936 tf
BC2801 tf
BC3244 tf
BC3891 tf
BC4661 tf
BC1969 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
4064 5.30e-01 gaggtAt.gatagaaAAGgagGc
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4065 2.00e+02 CAAgAtgAatgGAGgtA
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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 72 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.93e-02 3.89e-02 10/36
Global kegg category 1.73e-02 3.57e-02 9/36
Metabolism kegg subcategory 1.73e-02 3.57e-02 9/36
Metabolic pathways kegg pathway 2.42e-02 4.57e-02 8/36
Biosynthesis of secondary metabolites kegg pathway 3.96e-03 1.30e-02 6/36

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Unknown function tigr mainrole 2.00e-06 5.00e-06 6/36
Enzymes of unknown specificity tigr sub1role 6.00e-06 1.90e-05 4/36

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.08e-02 3.40e-02 14/36
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 72

There are 36 genes in Module 72

Gene Member Table (36)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0044 BC0044 CDS None chromosome 43533 44297 + Sec-independent secretion protein tatD (NCBI ptt file) False
BC0196 BC0196 CDS None chromosome 171581 172249 - ABC transporter permease protein (NCBI ptt file) False
BC0264 BC0264 CDS None chromosome 238627 239796 + Alanine racemase (NCBI ptt file) False
BC0327 BC0327 CDS None chromosome 302724 302978 + Phosphorybosylformylglycinamidine synthetase, PurS component (NCBI ptt file) False
BC0328 BC0328 CDS None chromosome 302975 303658 + Phosphoribosylformylglycinamidine synthase (NCBI ptt file) False
BC0353 BC0353 CDS None chromosome 331346 332251 + hypothetical protein (NCBI ptt file) False
BC0358 BC0358 CDS None chromosome 337629 337952 + Quaternary ammonium compound-resistance protein (NCBI ptt file) False
BC0395 BC0395 CDS None chromosome 374160 374792 - Metal-dependent hydrolase (NCBI ptt file) False
BC0411 BC0411 CDS None chromosome 392479 393162 + hypothetical protein (NCBI ptt file) False
BC0802 BC0802 CDS None chromosome 784588 785583 + Alcohol dehydrogenase (NCBI ptt file) False
BC0979 BC0979 CDS None chromosome 965113 966111 - Dihydroxyacetone kinase (NCBI ptt file) False
BC1069 BC1069 CDS None chromosome 1053588 1054505 + Ferrochelatase (NCBI ptt file) False
BC1202 BC1202 CDS None chromosome 1182712 1183452 - Serine/threonine protein phosphatase (NCBI ptt file) False
BC2025 BC2025 CDS None chromosome 1969460 1970446 + hypothetical protein (NCBI ptt file) False
BC2046 BC2046 CDS None chromosome 1988837 1989484 + CBS domain containing protein (NCBI ptt file) False
BC2174 BC2174 CDS None chromosome 2123542 2124264 + Phosphoglycolate phosphatase (NCBI ptt file) False
BC2462 BC2462 CDS None chromosome 2426217 2426723 + Ribosomal-protein-serine acetyltransferase (NCBI ptt file) False
BC2701 BC2701 CDS None chromosome 2684442 2684807 - hypothetical protein (NCBI ptt file) False
BC2702 BC2702 CDS None chromosome 2684865 2685062 - hypothetical protein (NCBI ptt file) False
BC2830 BC2830 CDS None chromosome 2793898 2794263 - DNA-binding protein (NCBI ptt file) False
BC2877 BC2877 CDS None chromosome 2836874 2837644 - Zwittermicin A resistance protein ZmaR (NCBI ptt file) False
BC3014 BC3014 CDS None chromosome 2977935 2978441 - hypothetical protein (NCBI ptt file) False
BC3174 BC3174 CDS None chromosome 3144262 3145026 - Short chain type dehydrogenase/reductase (NCBI ptt file) False
BC3216 BC3216 CDS None chromosome 3196438 3197433 - 1-aminocyclopropane-1-carboxylate deaminase (NCBI ptt file) False
BC3246 BC3246 CDS None chromosome 3225549 3226058 - hypothetical protein (NCBI ptt file) False
BC3316 BC3316 CDS None chromosome 3282276 3282752 - Regulatory protein (NCBI ptt file) False
BC3365 BC3365 CDS None chromosome 3327439 3327975 - hypothetical protein (NCBI ptt file) False
BC3476 BC3476 CDS None chromosome 3429452 3430345 - Transcriptional regulators, LysR family (NCBI ptt file) True
BC3477 BC3477 CDS None chromosome 3430469 3431434 + Quinone oxidoreductase (NCBI ptt file) False
BC3989 BC3989 CDS None chromosome 3963172 3964389 - Diguanylate cyclase/phosphodiesterase domain 2 (EAL) (NCBI ptt file) False
BC4223 BC4223 CDS None chromosome 4172814 4173038 - hypothetical protein (NCBI ptt file) False
BC4255 BC4255 CDS None chromosome 4202359 4202871 + Isochorismatase (NCBI ptt file) False
BC4260 BC4260 CDS None chromosome 4205914 4206897 - Glucokinase (NCBI ptt file) False
BC4305 BC4305 CDS None chromosome 4247773 4248399 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC4404 BC4404 CDS None chromosome 4345747 4346640 - Cobalt-zinc-cadmium resistance protein czcD (NCBI ptt file) False
BC5436 BC5436 CDS None chromosome 5358764 5359729 - Peptide methionine sulfoxide reductase (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 72

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.