Organism : Bacillus cereus ATCC14579 | Module List:
Module 225 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 225

There are 11 regulatory influences for Module 225

Regulator Table (11)
Regulator Name Type
BC2794 tf
BC0082 tf
BC0598 tf
BC2340 tf
BC3244 tf
BC0473 tf
BC2386 tf
BC3826 tf
BC0950 tf
BC4652 tf
BC1915 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
4366 1.80e+04 CATGTGTcAAGcG
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4367 3.60e+03 AAggaGtGaaT
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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 225 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Arginine and proline metabolism kegg pathway 5.82e-04 4.12e-03 3/34

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Function unknown cog subcategory 3.10e-02 4.90e-02 5/34
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 225

There are 34 genes in Module 225

Gene Member Table (34)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0012 BC0012 CDS None chromosome 14232 15233 - IG hypothetical 16768 (NCBI ptt file) False
BC0044 BC0044 CDS None chromosome 43533 44297 + Sec-independent secretion protein tatD (NCBI ptt file) False
BC0048 BC0048 CDS None chromosome 47145 47405 + VEG protein (NCBI ptt file) False
BC0231 BC0231 CDS None chromosome 205829 206158 + hypothetical protein (NCBI ptt file) False
BC0413 BC0413 CDS None chromosome 394860 396530 + Exo-alpha-1,4-glucosidase (NCBI ptt file) False
BC0603 BC0603 CDS None chromosome 594427 594975 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC0836 BC0836 DUMMY None chromosome 0 0 + None False
BC0900 BC0900 CDS None chromosome 888332 888511 - hypothetical protein (NCBI ptt file) False
BC0974 BC0974 CDS None chromosome 961911 962177 - hypothetical protein (NCBI ptt file) False
BC1616 BC1616 CDS None chromosome 1574509 1575174 - hypothetical Membrane Associated Protein (NCBI ptt file) False
BC1713 BC1713 CDS None chromosome 1661921 1662343 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC1714 BC1714 CDS None chromosome 1662574 1662693 - hypothetical protein (NCBI ptt file) False
BC2015 BC2015 CDS None chromosome 1960375 1960566 - hypothetical protein (NCBI ptt file) False
BC2020 BC2020 CDS None chromosome 1965032 1965502 - Spermine/spermidine acetyltransferase (NCBI ptt file) False
BC2040 BC2040 CDS None chromosome 1984098 1984556 + putative spore coat protein (NCBI ptt file) False
BC2115 BC2115 CDS None chromosome 2056039 2058267 - Transglutaminase-like enzymes, hypothetical cysteine proteases (NCBI ptt file) False
BC2190 BC2190 CDS None chromosome 2136189 2137646 - Penicillin-binding protein (NCBI ptt file) False
BC2226 BC2226 CDS None chromosome 2171897 2172574 - hypothetical protein (NCBI ptt file) False
BC2298 BC2298 CDS None chromosome 2243011 2243310 + Transcriptional repressor (NCBI ptt file) True
BC2428 BC2428 CDS None chromosome 2372641 2373123 - hypothetical protein (NCBI ptt file) False
BC2507 BC2507 CDS None chromosome 2475653 2476495 - Transcriptional regulator, AraC family (NCBI ptt file) True
BC2606 BC2606 CDS None chromosome 2570361 2570573 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC2663 BC2663 DUMMY None chromosome 0 0 + None False
BC3040 BC3040 CDS None chromosome 2999850 3000290 + EMG2 protein (NCBI ptt file) False
BC3236 BC3236 CDS None chromosome 3215986 3216318 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC3452 BC3452 CDS None chromosome 3408952 3409446 + hypothetical protein (NCBI ptt file) False
BC3715 BC3715 CDS None chromosome 3680701 3680946 + hypothetical protein (NCBI ptt file) False
BC3739 BC3739 CDS None chromosome 3703550 3704308 - Exodeoxyribonuclease III (NCBI ptt file) False
BC3763 BC3763 DUMMY None chromosome 0 0 + None False
BC4002 BC4002 CDS None chromosome 3977069 3977257 - hypothetical protein (NCBI ptt file) False
BC4257 BC4257 CDS None chromosome 4203738 4204850 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC4564 BC4564 CDS None chromosome 4510754 4511311 + Metal-dependent phosphohydrolase (NCBI ptt file) False
BC4582 BC4582 CDS None chromosome 4527186 4527578 - S-adenosylmethionine decarboxylase proenzyme (NCBI ptt file) False
BC5214 BC5214 CDS None chromosome 5115622 5115993 + S-adenosylmethionine decarboxylase proenzyme (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 225

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.