Organism : Bacillus cereus ATCC14579 | Module List:
Module 86 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 86

There are 11 regulatory influences for Module 86

Regulator Table (11)
Regulator Name Type
BC0566 tf
BC3155 tf
BC1037 tf
BC3792 tf
BC0840 tf
BC3589 tf
BC3255 tf
BC5222 tf
BC3903 tf
BC3033 tf
BC0047 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
4090 1.00e+02 GatgGAgtaGa
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4091 1.40e+04 CcGAAccGGAcCc
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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 86 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 2.40e-05 4.10e-04 8/31
Membrane Transport kegg subcategory 1.60e-05 2.95e-04 7/31
ABC transporters kegg pathway 5.00e-06 1.11e-04 7/31
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

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 0.00e+00 1.00e-06 7/31
Anions tigr sub1role 0.00e+00 0.00e+00 7/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.88e-02 4.59e-02 12/31
Inorganic ion transport and metabolism cog subcategory 0.00e+00 1.00e-06 9/31
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 86

There are 31 genes in Module 86

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0204 BC0204 CDS None chromosome 180157 181407 + Bicyclomycin resistance protein (NCBI ptt file) False
BC0710 BC0710 CDS None chromosome 711218 712147 + Phosphate-binding protein (NCBI ptt file) False
BC0711 BC0711 CDS None chromosome 712216 713109 + Phosphate transport system permease protein pstC (NCBI ptt file) False
BC0712 BC0712 CDS None chromosome 713112 714032 + Phosphate transport system permease protein pstA (NCBI ptt file) False
BC0791 BC0791 CDS None chromosome 776217 777881 + NADH dehydrogenase (NCBI ptt file) False
BC0829 BC0829 CDS None chromosome 810600 810968 + hypothetical protein (NCBI ptt file) False
BC0830 BC0830 CDS None chromosome 810989 811333 + hypothetical protein (NCBI ptt file) False
BC0876 BC0876 CDS None chromosome 853895 854143 + hypothetical protein (NCBI ptt file) False
BC1037 BC1037 CDS None chromosome 1019261 1019602 + Transcriptional regulator, PadR family (NCBI ptt file) True
BC1038 BC1038 CDS None chromosome 1019595 1020371 + Teicoplanin resistance protein vanZ (NCBI ptt file) False
BC1230 BC1230 CDS None chromosome 1204867 1205265 - Bacterial Ig-like domain protein (NCBI ptt file) False
BC1817 BC1817 CDS None chromosome 1774467 1775117 - CAAX amino terminal protease family (NCBI ptt file) False
BC2069 BC2069 CDS None chromosome 2011886 2012308 + Acetyltransferase (NCBI ptt file) False
BC2106 BC2106 CDS None chromosome 2048170 2048808 - hypothetical protein (NCBI ptt file) False
BC2107 BC2107 CDS None chromosome 2048838 2049824 - Quinone oxidoreductase (NCBI ptt file) False
BC2130 BC2130 CDS None chromosome 2074490 2075407 + Transporter (NCBI ptt file) False
BC2131 BC2131 CDS None chromosome 2075601 2076053 + hypothetical protein (NCBI ptt file) False
BC2377 BC2377 CDS None chromosome 2321386 2322174 - hypothetical protein (NCBI ptt file) False
BC2542 BC2542 CDS None chromosome 2515915 2516499 + Acetyltransferase (NCBI ptt file) False
BC3447 BC3447 CDS None chromosome 3405576 3406619 - CzcD accessory protein (NCBI ptt file) False
BC3640 BC3640 CDS None chromosome 3609156 3609527 - Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily (NCBI ptt file) False
BC3729 BC3729 CDS None chromosome 3693891 3694373 - Acetyltransferase (NCBI ptt file) False
BC4266 BC4266 CDS None chromosome 4211767 4212582 - Phosphate transport ATP-binding protein pstB (NCBI ptt file) False
BC4267 BC4267 CDS None chromosome 4212611 4213468 - Phosphate transport system permease protein pstA (NCBI ptt file) False
BC4268 BC4268 CDS None chromosome 4213479 4214429 - Phosphate transport system permease protein pstC (NCBI ptt file) False
BC4269 BC4269 CDS None chromosome 4214457 4215374 - Phosphate-binding protein (NCBI ptt file) False
BC4343 BC4343 CDS None chromosome 4282384 4283769 - Alkaline phosphatase (NCBI ptt file) False
BC4755 BC4755 CDS None chromosome 4690189 4690722 + Phosphatidylglycerophosphatase B (NCBI ptt file) False
BC4756 BC4756 CDS None chromosome 4690732 4691877 + Glycosyltransferase (NCBI ptt file) False
BC4769 BC4769 CDS None chromosome 4701779 4702840 + Collagen triple helix repeat protein (NCBI ptt file) False
BC5071 BC5071 CDS None chromosome 4977297 4978499 - Macrolide-efflux 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 86

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.