Organism : Bacillus cereus ATCC14579 | Module List:
Module 415 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 415

There are 16 regulatory influences for Module 415

Regulator Table (16)
Regulator Name Type
BC3332 tf
BC2680 tf
BC3039 tf
BC1439 tf
BC1449 tf
BC2133 tf
BC1969 tf
BC5250 tf
BC1302 tf
BC3756 tf
BC4842 tf
BC2766 tf
BC4374 tf
BC0477 tf
BC1842 tf
BC5361 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
4740 4.50e-04 aAGGaGg
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4741 1.10e+03 cTaTcaTtcCcCt.T
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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 415 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 415

There are 30 genes in Module 415

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0261 BC0261 CDS None chromosome 236377 236949 - hypothetical membrane protein (Rhomboid family) (NCBI ptt file) False
BC0313 BC0313 CDS None chromosome 283028 283804 - Methyltransferase (NCBI ptt file) False
BC0319 BC0319 CDS None chromosome 292315 293106 - hypothetical protein (NCBI ptt file) False
BC0791 BC0791 CDS None chromosome 776217 777881 + NADH dehydrogenase (NCBI ptt file) False
BC0891 BC0891 CDS None chromosome 877422 877619 - hypothetical protein (NCBI ptt file) False
BC0987 BC0987 CDS None chromosome 972793 973182 + hypothetical protein (NCBI ptt file) False
BC2106 BC2106 CDS None chromosome 2048170 2048808 - hypothetical protein (NCBI ptt file) False
BC2110 BC2110 CDS None chromosome 2051392 2053071 - ABC1 family protein (NCBI ptt file) False
BC2269 BC2269 CDS None chromosome 2212699 2212893 - hypothetical protein (NCBI ptt file) False
BC2424 BC2424 CDS None chromosome 2366583 2367014 + hypothetical protein (NCBI ptt file) False
BC2653 BC2653 CDS None chromosome 2635107 2635586 + hypothetical protein (NCBI ptt file) False
BC2764 BC2764 CDS None chromosome 2740136 2740480 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC2765 BC2765 CDS None chromosome 2740512 2740769 - hypothetical protein (NCBI ptt file) False
BC2766 BC2766 CDS None chromosome 2740882 2742732 - Sigma-54-dependent transcriptional activator (NCBI ptt file) True
BC2956 BC2956 CDS None chromosome 2913737 2914021 + hypothetical protein (NCBI ptt file) False
BC3245 BC3245 CDS None chromosome 3223389 3224684 + Amino acid permease (NCBI ptt file) False
BC3349 BC3349 CDS None chromosome 3313691 3314884 + Transporter, MFS superfamily (NCBI ptt file) False
BC3445 BC3445 CDS None chromosome 3404764 3404958 + hypothetical protein (NCBI ptt file) False
BC3640 BC3640 CDS None chromosome 3609156 3609527 - Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily (NCBI ptt file) False
BC3689 BC3689 CDS None chromosome 3656256 3656912 - Site-specific recombinase (NCBI ptt file) False
BC3732 BC3732 CDS None chromosome 3697456 3697758 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC3879 BC3879 CDS None chromosome 3859436 3860821 + Transporter (NCBI ptt file) False
BC4651 BC4651 CDS None chromosome 4593110 4594054 + Transporter, Drug/Metabolite Exporter family (NCBI ptt file) False
BC4852 BC4852 CDS None chromosome 4776349 4776573 + hypothetical protein (NCBI ptt file) False
BC4868 BC4868 CDS None chromosome 4795076 4795681 + Cell envelope-bound metalloprotease (camelysin) (NCBI ptt file) False
BC4941 BC4941 CDS None chromosome 4858390 4859187 + YbbM family integral membrane protein (NCBI ptt file) False
BC5029 BC5029 CDS None chromosome 4930153 4931595 + Sensor protein vanSB (NCBI ptt file) False
BC5030 BC5030 CDS None chromosome 4931736 4932638 + Transporter, Drug/Metabolite Exporter family (NCBI ptt file) False
BC5058 BC5058 CDS None chromosome 4965197 4966411 - Chloramphenicol resistance protein (NCBI ptt file) False
BC5316 BC5316 CDS None chromosome 5224689 5225933 - Serine hydroxymethyltransferase (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 415

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.