Organism : Bacillus cereus ATCC14579 | Module List:
Module 264 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 264

There are 14 regulatory influences for Module 264

Regulator Table (14)
Regulator Name Type
BC3244 tf
BC4104 tf
BC1134 tf
BC3224 tf
BC4525 tf
BC4826 tf
BC2558 tf
BC0057 tf
BC1732 tf
BC5010 tf
BC1936 tf
BC3653 tf
BC3062 tf
BC4425 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
4444 9.60e-05 aAaAGggG
Loader icon
4445 3.80e+04 cTAGGTGtGGC
Loader icon
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 264 is enriched for following functions.

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 264

There are 32 genes in Module 264

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0185 BC0185 CDS None chromosome 158260 159153 + Arginase (NCBI ptt file) False
BC0238 BC0238 CDS None chromosome 213132 213266 + hypothetical protein (NCBI ptt file) False
BC0520 BC0520 CDS None chromosome 509261 509623 - hypothetical protein (NCBI ptt file) False
BC0800 BC0800 CDS None chromosome 782485 782925 - hypothetical protein (NCBI ptt file) False
BC1039 BC1039 CDS None chromosome 1020811 1020975 - hypothetical protein (NCBI ptt file) False
BC1134 BC1134 CDS None chromosome 1114632 1115213 + Competence transcription factor (NCBI ptt file) True
BC1266 BC1266 CDS None chromosome 1243083 1244315 - Integral membrane protein (NCBI ptt file) False
BC1349 BC1349 CDS None chromosome 1322851 1323429 - Acetyltransferase (NCBI ptt file) False
BC1389 BC1389 CDS None chromosome 1352008 1353243 - Proton/sodium-glutamate symport protein (NCBI ptt file) False
BC1782 BC1782 CDS None chromosome 1735409 1735636 - hypothetical protein (NCBI ptt file) False
BC1783 BC1783 CDS None chromosome 1735689 1736792 - Capsule biosynthesis protein capA (NCBI ptt file) False
BC1962 BC1962 CDS None chromosome 1909530 1910138 - Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) False
BC2147 BC2147 CDS None chromosome 2091417 2092490 + Response regulator aspartate phosphatase (NCBI ptt file) False
BC2148 BC2148 CDS None chromosome 2092487 2092612 + Response regulator aspartate phosphatase inhibitor (NCBI ptt file) False
BC2959 BC2959 CDS None chromosome 2916289 2917782 + Malate:quinone oxidoreductase (NCBI ptt file) False
BC3224 BC3224 CDS None chromosome 3205919 3206542 + Transcriptional regulator, ArsR family (NCBI ptt file) True
BC3264 BC3264 CDS None chromosome 3246518 3247225 + hypothetical protein (NCBI ptt file) False
BC3921 BC3921 CDS None chromosome 3905613 3906086 + Acetyltransferase (NCBI ptt file) False
BC3938 BC3938 CDS None chromosome 3917781 3918146 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC4007 BC4007 CDS None chromosome 3981594 3982868 - Sporulation kinase B (NCBI ptt file) False
BC4041 BC4041 CDS None chromosome 4013985 4014317 - hypothetical protein (NCBI ptt file) False
BC4063 BC4063 CDS None chromosome 4034707 4035492 - hydrolase (HAD superfamily) (NCBI ptt file) False
BC4195 BC4195 CDS None chromosome 4153480 4154058 + Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) False
BC4558 BC4558 CDS None chromosome 4503465 4503572 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC4578 BC4578 CDS None chromosome 4523678 4523875 + hypothetical protein (NCBI ptt file) False
BC4658 BC4658 CDS None chromosome 4600018 4600578 - Maltose O-acetyltransferase (NCBI ptt file) False
BC4676 BC4676 CDS None chromosome 4615582 4615911 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC4677 BC4677 CDS None chromosome 4615908 4616420 - General stress protein (NCBI ptt file) False
BC4923 BC4923 CDS None chromosome 4834131 4834448 - hypothetical protein (NCBI ptt file) False
BC4961 BC4961 CDS None chromosome 4872897 4873337 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC5093 BC5093 CDS None chromosome 4998622 4998933 + Xanthine permease (NCBI ptt file) False
BC5280 BC5280 CDS None chromosome 5190096 5190530 - (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase (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 264

Please add your comments for this module by using the form below. Your comments will be publicly available.

comments powered by Disqus
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.