Organism : Bacillus cereus ATCC14579 | Module List:
Module 453 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 453

There are 11 regulatory influences for Module 453

Regulator Table (11)
Regulator Name Type
BC2904 tf
BC3493 tf
BC2526 tf
BC1673 tf
BC4650 tf
BC3389 tf
BC4101 tf
BC2379 tf
BC0518 tf
BC2742 tf
BC0882 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
4816 9.00e+04 GAGGTGAGaG
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4817 3.00e+03 TaGGGGta
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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 453 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 2.71e-02 4.99e-02 4/32

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 453

There are 32 genes in Module 453

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0372 BC0372 CDS None chromosome 352532 353803 + hypothetical protein (NCBI ptt file) False
BC0687 BC0687 CDS None chromosome 686353 687900 - IG hypothetical 22578 (NCBI ptt file) False
BC0882 BC0882 CDS None chromosome 861347 862003 + Two-component response regulator comA (NCBI ptt file) True
BC0932 BC0932 CDS None chromosome 913918 914109 + hypothetical protein (NCBI ptt file) False
BC1065 BC1065 CDS None chromosome 1047962 1049377 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC1265 BC1265 CDS None chromosome 1241946 1242929 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC1943 BC1943 CDS None chromosome 1889875 1892436 + Glycosyltransferase (NCBI ptt file) False
BC1999 BC1999 CDS None chromosome 1946645 1947580 + IolS protein (NCBI ptt file) False
BC2090 BC2090 CDS None chromosome 2035571 2036392 + hypothetical protein (NCBI ptt file) False
BC2330 BC2330 CDS None chromosome 2280557 2281429 + Zn-dependent hydrolase (NCBI ptt file) False
BC2348 BC2348 CDS None chromosome 2296022 2296948 + Acetyltransferase (NCBI ptt file) False
BC2363 BC2363 CDS None chromosome 2307991 2309034 + Aspartate-semialdehyde dehydrogenase (NCBI ptt file) False
BC2407 BC2407 CDS None chromosome 2349915 2350184 + hypothetical protein (NCBI ptt file) False
BC2430 BC2430 CDS None chromosome 2373846 2374556 + Methyltransferase (NCBI ptt file) False
BC2742 BC2742 CDS None chromosome 2721793 2723226 + Transcriptional regulator, GntR family (NCBI ptt file) True
BC2810 BC2810 CDS None chromosome 2773505 2774506 - hypothetical protein (NCBI ptt file) False
BC2915 BC2915 CDS None chromosome 2872115 2872624 - hypothetical protein (NCBI ptt file) False
BC2923 BC2923 CDS None chromosome 2878196 2878696 - Acetyltransferase (NCBI ptt file) False
BC3014 BC3014 CDS None chromosome 2977935 2978441 - hypothetical protein (NCBI ptt file) False
BC3029 BC3029 CDS None chromosome 2990664 2991455 + hypothetical protein (NCBI ptt file) False
BC3150 BC3150 CDS None chromosome 3120012 3120593 - Transcriptional regulator, AraC family (NCBI ptt file) False
BC3170 BC3170 CDS None chromosome 3141374 3141535 - Transposase (NCBI ptt file) False
BC3216 BC3216 CDS None chromosome 3196438 3197433 - 1-aminocyclopropane-1-carboxylate deaminase (NCBI ptt file) False
BC3322 BC3322 CDS None chromosome 3287082 3287363 + hypothetical protein (NCBI ptt file) False
BC3366 BC3366 CDS None chromosome 3327995 3328816 - oxetanocin A resistance protein (NCBI ptt file) False
BC3446 BC3446 CDS None chromosome 3405047 3405295 - hypothetical protein (NCBI ptt file) False
BC3457 BC3457 CDS None chromosome 3414132 3414698 + hypothetical protein (NCBI ptt file) False
BC3687 BC3687 CDS None chromosome 3654348 3655931 + 2',3'-cyclic-nucleotide 2'-phosphodiesterase (NCBI ptt file) False
BC3919 BC3919 CDS None chromosome 3902736 3904352 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC4818 BC4818 CDS None chromosome 4740665 4741345 - hypothetical protein (NCBI ptt file) False
BC4839 BC4839 CDS None chromosome 4761046 4761798 + ABC transporter ATP-binding protein (NCBI ptt file) False
BC5031 BC5031 CDS None chromosome 4933002 4934636 - Methionyl-tRNA synthetase (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 453

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.