Organism : Bacillus cereus ATCC14579 | Module List:
Module 213 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 213

There are 15 regulatory influences for Module 213

Regulator Table (15)
Regulator Name Type
BC0954 tf
BC0613 tf
BC1884 tf
BC4652 tf
BC0648 tf
BC1622 tf
BC0410 tf
BC1356 tf
BC0595 tf
BC0980 tf
BC3961 tf
BC2794 tf
BC3332 tf
BC0975 tf
BC1296 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
4342 9.90e+02 tagAgggagatgaaa
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4343 7.50e+03 GcGcCcCC
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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 213 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Environmental Information Processing kegg category 2.35e-02 4.48e-02 4/31
Signal Transduction kegg subcategory 1.30e-03 6.72e-03 3/31
Two-component system kegg pathway 1.30e-03 6.72e-03 3/31
Cellular Processes kegg category 1.59e-04 1.67e-03 3/31
Cell Motility kegg subcategory 1.59e-04 1.67e-03 3/31
Bacterial chemotaxis kegg pathway 1.60e-05 2.96e-04 3/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 3.81e-03 6.94e-03 4/31
Cell motility cog subcategory 1.35e-04 3.32e-04 3/31
Methyl-accepting chemotaxis protein cog 0.00e+00 2.00e-06 3/31
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 213

There are 31 genes in Module 213

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0422 BC0422 CDS None chromosome 408375 410117 + Methyl-accepting chemotaxis protein (NCBI ptt file) False
BC0423 BC0423 CDS None chromosome 410851 413832 + Peptide synthetase (NCBI ptt file) False
BC0757 BC0757 CDS None chromosome 744475 745656 - Bicyclomycin resistance protein (NCBI ptt file) False
BC0954 BC0954 CDS None chromosome 942294 943040 + tcdA-E operon negative regulator (NCBI ptt file) True
BC0965 BC0965 CDS None chromosome 953514 954101 + hypothetical protein (NCBI ptt file) False
BC0966 BC0966 CDS None chromosome 954158 954820 + Fimbria associated protein (NCBI ptt file) False
BC0992 BC0992 CDS None chromosome 978302 978985 + hypothetical protein (NCBI ptt file) False
BC1126 BC1126 CDS None chromosome 1107737 1108402 + S-layer homology domain (NCBI ptt file) False
BC2006 BC2006 CDS None chromosome 1952576 1954558 + Methyl-accepting chemotaxis protein (NCBI ptt file) False
BC2047 BC2047 CDS None chromosome 1989941 1991278 + Branched-chain amino acid transport system carrier protein (NCBI ptt file) False
BC2184 BC2184 CDS None chromosome 2131289 2131999 + ABC-type transporter ATP-binding protein ecsA (NCBI ptt file) False
BC2408 BC2408 CDS None chromosome 2350258 2351634 + ATP-dependent RNA helicase (NCBI ptt file) False
BC2415 BC2415 CDS None chromosome 2357354 2357845 - Collagen triple helix repeat protein (NCBI ptt file) False
BC2667 BC2667 CDS None chromosome 2651521 2652327 + DEGV protein (NCBI ptt file) False
BC2721 BC2721 CDS None chromosome 2697648 2698310 - Serine/threonine protein kinases (NCBI ptt file) False
BC2771 BC2771 CDS None chromosome 2744986 2745477 + hypothetical Exported Protein (NCBI ptt file) False
BC3122 BC3122 CDS None chromosome 3091993 3092829 - Arylesterase (NCBI ptt file) False
BC3186 BC3186 CDS None chromosome 3157553 3158254 - hypothetical protein (NCBI ptt file) False
BC3189 BC3189 CDS None chromosome 3163950 3165269 + Serine transporter (NCBI ptt file) False
BC3495 BC3495 CDS None chromosome 3450337 3451281 - Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) False
BC3505 BC3505 CDS None chromosome 3460482 3460880 - hypothetical protein (NCBI ptt file) False
BC3631 BC3631 CDS None chromosome 3603220 3604194 - Medium-chain-fatty-acid--CoA ligase (NCBI ptt file) False
BC3874 BC3874 CDS None chromosome 3855326 3856507 - hypothetical protein (NCBI ptt file) False
BC4530 BC4530 CDS None chromosome 4476523 4477422 - hypothetical protein (NCBI ptt file) False
BC4596 BC4596 CDS None chromosome 4542008 4542469 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC5051 BC5051 CDS None chromosome 4954735 4956177 - Sodium/proton-dependent alanine carrier protein (NCBI ptt file) False
BC5055 BC5055 CDS None chromosome 4958927 4962568 - Wall-associated protein precursor (NCBI ptt file) False
BC5065 BC5065 CDS None chromosome 4972855 4974357 - Methyl-accepting chemotaxis protein (NCBI ptt file) False
BC5259 BC5259 CDS None chromosome 5166958 5167992 - ABC transporter substrate-binding protein (NCBI ptt file) False
BC5261 BC5261 CDS None chromosome 5168838 5170268 - Two component system histidine kinase (NCBI ptt file) False
BC5264 BC5264 CDS None chromosome 5172149 5172979 - EPSX protein (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 213

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.