Organism : Bacillus cereus ATCC14579 | Module List:
Module 419 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 419

There are 9 regulatory influences for Module 419

Regulator Table (9)
Regulator Name Type
BC3253 tf
BC0213 tf
BC5000 tf
BC4076 tf
BC2672 tf
BC1131 tf
BC0230 tf
BC5409 tf
BC2794 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
4748 1.60e-10 TTGAcAATGAtAATcAaTtTCAaT
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4749 1.60e+02 TGAtAAtgataATCAaT
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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 419 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Terpenoids and Polyketides kegg subcategory 6.62e-04 4.41e-03 3/28
Biosynthesis of siderophore group nonribosomal peptides kegg pathway 0.00e+00 8.00e-06 3/28
Environmental Information Processing kegg category 0.00e+00 4.00e-06 10/28
Membrane Transport kegg subcategory 0.00e+00 0.00e+00 10/28
ABC transporters kegg pathway 0.00e+00 0.00e+00 10/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.20e-05 5.00e-05 17/28
Coenzyme transport and metabolism cog subcategory 7.07e-03 1.24e-02 3/28
Inorganic ion transport and metabolism cog subcategory 0.00e+00 0.00e+00 10/28
Secondary metabolites biosynthesis, transport and catabolism cog subcategory 6.70e-05 1.84e-04 4/28
ABC-type Fe3+-siderophore transport system, permease component cog 0.00e+00 0.00e+00 4/28
ABC-type Fe3+-hydroxamate transport system, periplasmic component cog 0.00e+00 1.00e-06 3/28
ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components cog 0.00e+00 0.00e+00 3/28
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 419

There are 28 genes in Module 419

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC1331 BC1331 CDS None chromosome 1306926 1309208 + Internalin (NCBI ptt file) False
BC1375 BC1375 CDS None chromosome 1343905 1344081 + hypothetical protein (NCBI ptt file) False
BC1376 BC1376 CDS None chromosome 1344074 1344520 + Flavodoxin (NCBI ptt file) False
BC1377 BC1377 CDS None chromosome 1344545 1345318 + hypothetical protein (NCBI ptt file) False
BC2304 BC2304 CDS None chromosome 2248764 2250380 + 2,3-dihydroxybenzoate-AMP ligase (NCBI ptt file) False
BC2305 BC2305 CDS None chromosome 2250405 2251298 + Isochorismatase (NCBI ptt file) False
BC2306 BC2306 CDS None chromosome 2251332 2255282 + Glycine-AMP ligase (NCBI ptt file) False
BC2307 BC2307 CDS None chromosome 2255886 2257991 + Glycine-AMP ligase (NCBI ptt file) False
BC2308 BC2308 CDS None chromosome 2258018 2258491 + Glycine-AMP ligase (NCBI ptt file) False
BC2309 BC2309 CDS None chromosome 2258488 2258712 + Antibiotic/siderophore biosynthesis protein (NCBI ptt file) False
BC2310 BC2310 CDS None chromosome 2258712 2260142 + Multidrug resistance protein B (NCBI ptt file) False
BC3466 BC3466 CDS None chromosome 3420793 3421701 - Ferrichrome-binding protein (NCBI ptt file) False
BC3467 BC3467 CDS None chromosome 3421723 3422739 - Ferrichrome transport system permease protein fhuG (NCBI ptt file) False
BC3468 BC3468 CDS None chromosome 3422740 3423774 - Ferrichrome transport system permease protein fhuB (NCBI ptt file) False
BC3540 BC3540 CDS None chromosome 3506561 3507460 - BNR-repeat containing protein (NCBI ptt file) False
BC3541 BC3541 CDS None chromosome 3507477 3507941 - Flavodoxin (NCBI ptt file) False
BC3734 BC3734 CDS None chromosome 3698562 3699380 - IroE protein (NCBI ptt file) False
BC3735 BC3735 CDS None chromosome 3699396 3700217 - Iron(III) dicitrate transport ATP-binding protein fecE (NCBI ptt file) False
BC4360 BC4360 CDS None chromosome 4299765 4300160 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC4361 BC4361 CDS None chromosome 4300127 4300945 - Ferrichrome transport ATP-binding protein fhuC (NCBI ptt file) False
BC4362 BC4362 CDS None chromosome 4300932 4301969 - Ferrichrome transport system permease protein fhuB (NCBI ptt file) False
BC4363 BC4363 CDS None chromosome 4301966 4302913 - Ferrichrome-binding protein (NCBI ptt file) False
BC4542 BC4542 CDS None chromosome 4485883 4486206 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC4543 BC4543 CDS None chromosome 4486279 4487043 - hypothetical Exported Protein (NCBI ptt file) False
BC4544 BC4544 CDS None chromosome 4487076 4487846 - Ferrichrome transport ATP-binding protein fhuC (NCBI ptt file) False
BC4545 BC4545 CDS None chromosome 4487836 4488819 - Ferrichrome transport system permease protein fhuB (NCBI ptt file) False
BC4546 BC4546 CDS None chromosome 4488847 4489722 - Ferrichrome-binding protein (NCBI ptt file) False
BC4547 BC4547 CDS None chromosome 4489798 4492512 - Cell surface 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 419

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.