Organism : Bacillus cereus ATCC14579 | Module List:
Module 65 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 65

There are 9 regulatory influences for Module 65

Regulator Table (9)
Regulator Name Type
BC0566 tf
BC3155 tf
BC1037 tf
BC3792 tf
BC3095 tf
BC3903 tf
BC0840 tf
BC2964 tf
BC0848 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
4050 3.10e+02 GGGaGGaGA
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4051 2.50e+02 gGAGagag
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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 65 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 0.00e+00 0.00e+00 15/28
Membrane Transport kegg subcategory 0.00e+00 0.00e+00 14/28
ABC transporters kegg pathway 0.00e+00 0.00e+00 14/28
Signal Transduction kegg subcategory 8.79e-04 5.26e-03 3/28
Two-component system kegg pathway 8.79e-04 5.26e-03 3/28

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 0.00e+00 11/28
Amino acids, peptides and amines tigr sub1role 2.70e-05 6.50e-05 3/28
Anions tigr sub1role 0.00e+00 0.00e+00 8/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.00e-06 1.00e-05 18/28
Carbohydrate transport and metabolism cog subcategory 5.53e-03 9.83e-03 4/28
Inorganic ion transport and metabolism cog subcategory 0.00e+00 0.00e+00 12/28
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 65

There are 28 genes in Module 65

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0566 BC0566 CDS None chromosome 549595 550161 + Glycerol uptake operon antiterminator regulatory protein (NCBI ptt file) True
BC0567 BC0567 CDS None chromosome 550158 551255 + SN-glycerol-3-phosphate transport ATP-binding protein ugpC (NCBI ptt file) False
BC0568 BC0568 CDS None chromosome 551255 552187 + SN-glycerol-3-phosphate transport system permease protein ugpA (NCBI ptt file) False
BC0569 BC0569 CDS None chromosome 552184 553005 + SN-glycerol-3-phosphate transport system permease protein ugpE (NCBI ptt file) False
BC0570 BC0570 CDS None chromosome 553027 554403 + Glycerol-3-phosphate-binding 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
BC0973 BC0973 CDS None chromosome 961178 961732 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC1028 BC1028 CDS None chromosome 1009547 1009747 + hypothetical protein (NCBI ptt file) False
BC1323 BC1323 CDS None chromosome 1298698 1299774 + 2-aminoethylphosphonate-binding protein (NCBI ptt file) False
BC1324 BC1324 CDS None chromosome 1299794 1300795 + 2-aminoethylphosphonate transport ATP-binding protein phnT (NCBI ptt file) False
BC1325 BC1325 CDS None chromosome 1300802 1302553 + 2-aminoethylphosphonate transport system permease protein phnU (NCBI ptt file) False
BC1705 BC1705 CDS None chromosome 1653213 1654400 - Low-affinity zinc transport protein (NCBI ptt file) False
BC2041 BC2041 CDS None chromosome 1984743 1984961 + hypothetical protein (NCBI ptt file) False
BC2131 BC2131 CDS None chromosome 2075601 2076053 + hypothetical protein (NCBI ptt file) False
BC3447 BC3447 CDS None chromosome 3405576 3406619 - CzcD accessory protein (NCBI ptt file) False
BC4265 BC4265 CDS None chromosome 4210819 4211475 - Phosphate transport system protein phoU (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
BC5021 BC5021 CDS None chromosome 4924454 4924765 + hypothetical protein (NCBI ptt file) False
BC5072 BC5072 CDS None chromosome 4978496 4980043 - ABC transporter ATP-binding 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 65

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.