Organism : Bacillus cereus ATCC14579 | Module List:
Module 47 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 47

There are 19 regulatory influences for Module 47

Regulator Table (19)
Regulator Name Type
BC4072 tf
BC2801 tf
BC0758 tf
BC2340 tf
BC0648 tf
BC0993 tf
BC0954 tf
BC3891 tf
BC0785 tf
BC3438 tf
BC4206 tf
BC1915 tf
BC3405 tf
BC2738 tf
BC3072 tf
BC3244 tf
BC5265 tf
BC3163 tf
BC0601 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
4014 8.00e-02 TCcTttt.TaT
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4015 8.10e+00 AGgAGG
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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 47 is enriched for following functions.

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 47

There are 29 genes in Module 47

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0483 BC0483 CDS None chromosome 472862 474133 + Penicillin-binding protein (NCBI ptt file) False
BC0601 BC0601 CDS None chromosome 591661 592362 + Transcriptional activator NprR (NCBI ptt file) True
BC0686 BC0686 CDS None chromosome 684608 686317 + hypothetical protein (NCBI ptt file) False
BC0758 BC0758 CDS None chromosome 745797 746258 + Transcriptional regulator, MarR family (NCBI ptt file) True
BC0901 BC0901 CDS None chromosome 888638 889687 + Deblocking aminopeptidase (NCBI ptt file) False
BC1275 BC1275 CDS None chromosome 1252752 1253507 - Methyltransferase (NCBI ptt file) False
BC1726 BC1726 CDS None chromosome 1672463 1673710 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC1994 BC1994 CDS None chromosome 1941592 1942410 - NH(3)-dependent NAD(+) synthetase (NCBI ptt file) False
BC2311 BC2311 CDS None chromosome 2260200 2260949 + 4'-phosphopantetheinyl transferase (NCBI ptt file) False
BC2312 BC2312 CDS None chromosome 2260975 2261517 + hypothetical protein (NCBI ptt file) False
BC2661 BC2661 CDS None chromosome 2643617 2644216 + Bacitracin transport permease protein BCRC (NCBI ptt file) False
BC2679 BC2679 CDS None chromosome 2663349 2663903 + hypothetical protein (NCBI ptt file) False
BC2686 BC2686 CDS None chromosome 2669964 2670410 + MutT/nudix family protein (NCBI ptt file) False
BC2714 BC2714 CDS None chromosome 2691637 2692215 - Acetyltransferase (NCBI ptt file) False
BC2804 BC2804 CDS None chromosome 2770387 2770752 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC2807 BC2807 CDS None chromosome 2771640 2772011 - hypothetical protein (NCBI ptt file) False
BC2808 BC2808 CDS None chromosome 2772008 2772790 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC3037 BC3037 CDS None chromosome 2996803 2997270 + Mutator mutT protein (7,8-dihydro-8-oxoguanine-triphosphatase) (NCBI ptt file) False
BC3070 BC3070 CDS None chromosome 3026485 3027036 - Signal peptidase I (NCBI ptt file) False
BC3071 BC3071 CDS None chromosome 3027060 3027737 - Copper homeostasis protein cutC (NCBI ptt file) False
BC3072 BC3072 CDS None chromosome 3027936 3028643 - Transcriptional regulator, ArsR family (NCBI ptt file) True
BC3073 BC3073 CDS None chromosome 3028713 3029183 + hypothetical protein (NCBI ptt file) False
BC3143 BC3143 CDS None chromosome 3116195 3116320 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC3144 BC3144 CDS None chromosome 3116403 3116558 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC3635 BC3635 CDS None chromosome 3606406 3606618 + hypothetical protein (NCBI ptt file) False
BC3727 BC3727 CDS None chromosome 3692648 3693463 + Formate transporter (NCBI ptt file) False
BC4125 BC4125 CDS None chromosome 4089923 4090474 - hypothetical protein (NCBI ptt file) False
BC4340 BC4340 CDS None chromosome 4280158 4280784 - NAD(P)H nitroreductase (NCBI ptt file) False
BC4897 BC4897 CDS None chromosome 4810807 4811220 - IG hypothetical 16740 (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 47

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.