Organism : Bacillus cereus ATCC14579 | Module List:
Module 28 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 28

There are 17 regulatory influences for Module 28

Regulator Table (17)
Regulator Name Type
BC5143 tf
BC2815 tf
BC4670 tf
BC4425 tf
BC5176 tf
BC0042 tf
BC5481 tf
BC3522 tf
BC0880 tf
BC0405 tf
BC5191 tf
BC4240 tf
BC2979 tf
BC1850 tf
BC5265 tf
BC2358 tf
BC1680 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
3978 8.60e+02 aAGaaGgA
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3979 4.10e+03 GGtAGCG
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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 28 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 1.90e-02 3.83e-02 3/27
Nucleotide Metabolism kegg subcategory 1.42e-04 1.52e-03 4/27
Purine metabolism kegg pathway 4.44e-04 3.45e-03 3/27
Pyrimidine metabolism kegg pathway 1.67e-04 1.72e-03 3/27
Genetic Information Processing kegg category 2.26e-02 4.35e-02 3/27
Biosynthesis of secondary metabolites kegg pathway 1.77e-02 3.63e-02 4/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 9.10e-05 1.95e-04 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 1.47e-02 2.47e-02 7/27
Transcription cog subcategory 6.06e-03 1.07e-02 5/27
Nucleotide transport and metabolism cog subcategory 1.37e-03 2.66e-03 3/27
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 28

There are 27 genes in Module 28

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0042 BC0042 CDS None chromosome 40611 40895 - Transcription state regulatory protein abrB (NCBI ptt file) True
BC0220 BC0220 CDS None chromosome 197851 198525 - Molybdenum transport system permease protein modB (NCBI ptt file) False
BC0466 BC0466 CDS None chromosome 455668 457188 + Fumarate hydratase (NCBI ptt file) False
BC0472 BC0472 CDS None chromosome 462449 462652 - hypothetical protein (NCBI ptt file) False
BC1387 BC1387 CDS None chromosome 1351253 1351675 + Transcriptional regulator, MarR family (NCBI ptt file) True
BC1463 BC1463 CDS None chromosome 1420990 1421697 - Purine nucleoside phosphorylase (NCBI ptt file) False
BC2153 BC2153 CDS None chromosome 2097299 2097553 + hypothetical protein (NCBI ptt file) False
BC2215 BC2215 CDS None chromosome 2159137 2160030 + Mechanosensitive ion channel (NCBI ptt file) False
BC2356 BC2356 CDS None chromosome 2303043 2303594 + Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) False
BC2437 BC2437 CDS None chromosome 2380112 2380288 + hypothetical protein (NCBI ptt file) False
BC2815 BC2815 CDS None chromosome 2780311 2782428 - ATP-dependent DNA helicase recQ (NCBI ptt file) True
BC4046 BC4046 CDS None chromosome 4018905 4019123 + hypothetical protein (NCBI ptt file) False
BC4085 BC4085 CDS None chromosome 4053308 4054612 - Pyrimidine-nucleoside phosphorylase (NCBI ptt file) False
BC4086 BC4086 CDS None chromosome 4054620 4055213 - Purine nucleoside phosphorylase (NCBI ptt file) False
BC4087 BC4087 CDS None chromosome 4055455 4056639 - Phosphopentomutase (NCBI ptt file) False
BC4139 BC4139 CDS None chromosome 4102596 4102847 + hypothetical protein (NCBI ptt file) False
BC4245 BC4245 CDS None chromosome 4191184 4191495 + hypothetical protein (NCBI ptt file) False
BC4384 BC4384 CDS None chromosome 4323755 4324099 + hypothetical protein (NCBI ptt file) False
BC4425 BC4425 CDS None chromosome 4367129 4367671 + hypothetical transcriptional regulator (NCBI ptt file) True
BC4610 BC4610 CDS None chromosome 4557882 4558157 - hypothetical protein (NCBI ptt file) False
BC5135 BC5135 CDS None chromosome 5037710 5039005 - Enolase (NCBI ptt file) False
BC5142 BC5142 CDS None chromosome 5044872 5045117 - Glutaredoxin (NCBI ptt file) False
BC5143 BC5143 CDS None chromosome 5045127 5046434 - RNA polymerase sigma-54 factor rpoN (NCBI ptt file) True
BC5176 BC5176 CDS None chromosome 5073645 5074013 + Transcriptional regulator, MerR family (NCBI ptt file) True
BC5177 BC5177 CDS None chromosome 5074018 5074563 + Trp repressor binding protein (NCBI ptt file) False
BC5317 BC5317 CDS None chromosome 5226184 5226774 - hypothetical protein (NCBI ptt file) False
BC5481 BC5481 CDS None chromosome 5402472 5403293 - Stage 0 sporulation protein J (NCBI ptt file) True

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 28

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.