Organism : Bacillus cereus ATCC14579 | Module List:
Module 60 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 60

There are 12 regulatory influences for Module 60

Regulator Table (12)
Regulator Name Type
BC4076 tf
BC0648 tf
BC4256 tf
BC2904 tf
BC1731 tf
BC0954 tf
BC4001 tf
BC2914 tf
BC2903 tf
BC4703 tf
BC4652 tf
BC1356 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
4040 2.70e+00 GagGGAg
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4041 3.20e+04 GGAGGC
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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 60 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 6.99e-03 1.23e-02 8/31
Defense mechanisms cog subcategory 9.40e-05 2.45e-04 4/31
ABC-type multidrug transport system, ATPase and permease components cog 0.00e+00 1.00e-06 3/31
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 60

There are 31 genes in Module 60

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0226 BC0226 CDS None chromosome 202977 203117 + hypothetical protein (NCBI ptt file) False
BC0648 BC0648 CDS None chromosome 642726 644150 + ECF-type sigma factor negative effector (NCBI ptt file) True
BC1060 BC1060 CDS None chromosome 1036938 1044272 + Collagen adhesion protein (NCBI ptt file) False
BC1072 BC1072 CDS None chromosome 1057746 1059962 + Endonuclease/Exonuclease/phosphatase family protein (NCBI ptt file) False
BC1447 BC1447 CDS None chromosome 1406133 1406750 + hypothetical protein (NCBI ptt file) False
BC1879 BC1879 CDS None chromosome 1829149 1829466 + Transglycosylase (NCBI ptt file) False
BC1955 BC1955 CDS None chromosome 1902505 1904121 + Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) False
BC2443 BC2443 CDS None chromosome 2384931 2385809 + Transcriptional regulator, XRE family (NCBI ptt file) False
BC2882 BC2882 CDS None chromosome 2841648 2842358 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC2902 BC2902 CDS None chromosome 2859769 2860641 - ABC transporter ATP-binding protein (NCBI ptt file) False
BC2904 BC2904 CDS None chromosome 2860822 2861019 - Transcriptional regulator, GntR family (NCBI ptt file) True
BC2913 BC2913 CDS None chromosome 2870560 2871288 - hypothetical protein (NCBI ptt file) False
BC2914 BC2914 CDS None chromosome 2871285 2871875 - Transcriptional regulator, TetR family (NCBI ptt file) True
BC3056 BC3056 CDS None chromosome 3013981 3014262 - hypothetical protein (NCBI ptt file) False
BC3085 BC3085 DUMMY None chromosome 0 0 + None False
BC3088 BC3088 CDS None chromosome 3045340 3046197 + Metal-dependent hydrolase (NCBI ptt file) False
BC3273 BC3273 CDS None chromosome 3252227 3252427 - hypothetical protein (NCBI ptt file) False
BC3276 BC3276 CDS None chromosome 3253802 3254185 - hypothetical protein (NCBI ptt file) False
BC3277 BC3277 CDS None chromosome 3254198 3255376 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC3678 BC3678 CDS None chromosome 3643942 3645660 - Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) False
BC3679 BC3679 CDS None chromosome 3645705 3647450 - Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) False
BC4027 BC4027 CDS None chromosome 4002405 4003166 - hypothetical protein (NCBI ptt file) False
BC4028 BC4028 CDS None chromosome 4003183 4003947 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC4076 BC4076 CDS None chromosome 4045486 4045911 + Acetoin transport repressor (NCBI ptt file) True
BC4172 BC4172 CDS None chromosome 4133561 4134859 - Stage IV sporulation protein B (NCBI ptt file) False
BC4264 BC4264 CDS None chromosome 4208124 4210478 - Phosphoglucomutase (NCBI ptt file) False
BC4299 BC4299 CDS None chromosome 4241574 4241927 - Diacylglycerol kinase (NCBI ptt file) False
BC4324 BC4324 CDS None chromosome 4267922 4268521 - ComE operon protein 1 (NCBI ptt file) False
BC4770 BC4770 CDS None chromosome 4703068 4704288 - Sporulation kinase (NCBI ptt file) False
BC4771 BC4771 CDS None chromosome 4704285 4705538 - Sporulation kinase (NCBI ptt file) False
BC5192 BC5192 CDS None chromosome 5091064 5091768 - Competence protein F (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 60

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.