Organism : Bacillus cereus ATCC14579 | Module List:
Module 76 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 76

There are 10 regulatory influences for Module 76

Regulator Table (10)
Regulator Name Type
BC1603 tf
BC0433 tf
BC5222 tf
BC0566 tf
BC4124 tf
BC4826 tf
BC4670 tf
BC1439 tf
BC1335 tf
BC4703 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
4072 1.50e+01 atCCtCcTc.TctaT.tatat
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4073 4.30e+03 CGCGGCG
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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 76 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 76

There are 35 genes in Module 76

Gene Member Table (35)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0166 BC0166 CDS None chromosome 145683 146111 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC0167 BC0167 CDS None chromosome 146178 146891 + Spore-specific N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) False
BC0260 BC0260 CDS None chromosome 235422 236384 + UV-endonuclease (UvsE/Uve1/UvdE Family) (NCBI ptt file) False
BC0398 BC0398 CDS None chromosome 377157 378467 - Benzoate transport protein (NCBI ptt file) False
BC0704 BC0704 DUMMY None chromosome 0 0 + None False
BC0856 BC0856 CDS None chromosome 831370 831708 - Transcriptional regulator, MarR family (NCBI ptt file) True
BC1170 BC1170 CDS None chromosome 1149553 1150287 + putative hydrolase (NCBI ptt file) False
BC1171 BC1171 CDS None chromosome 1150317 1151189 + Glucose epimerase (NCBI ptt file) False
BC1201 BC1201 DUMMY None chromosome 0 0 + None False
BC1204 BC1204 CDS None chromosome 1184928 1185854 - Glycosyltransferase (NCBI ptt file) False
BC1293 BC1293 CDS None chromosome 1271512 1272435 + Ribosomal large subunit pseudouridine synthase D (NCBI ptt file) False
BC1362 BC1362 CDS None chromosome 1333353 1333535 - hypothetical protein (NCBI ptt file) False
BC1434 BC1434 CDS None chromosome 1395001 1396317 + Na+/H+ antiporter NhaC (NCBI ptt file) False
BC1439 BC1439 CDS None chromosome 1399464 1400096 + Two-component response regulator yvqC (NCBI ptt file) True
BC1503 BC1503 CDS None chromosome 1457864 1458049 + hypothetical protein (NCBI ptt file) False
BC1631 BC1631 CDS None chromosome 1589125 1589841 + hypothetical protein (NCBI ptt file) False
BC1900 BC1900 DUMMY None chromosome 0 0 + None False
BC1970 BC1970 CDS None chromosome 1919205 1920002 + hypothetical protein (NCBI ptt file) False
BC2212 BC2212 CDS None chromosome 2157205 2157399 + hypothetical protein (NCBI ptt file) False
BC2359 BC2359 CDS None chromosome 2304506 2305402 + CAAX amino terminal protease family (NCBI ptt file) False
BC2555 BC2555 CDS None chromosome 2529308 2530009 + hypothetical protein (NCBI ptt file) False
BC2719 BC2719 CDS None chromosome 2695571 2696530 + Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) False
BC2741 BC2741 CDS None chromosome 2720727 2721644 - Transporter, Drug/Metabolite Exporter family (NCBI ptt file) False
BC2838 BC2838 CDS None chromosome 2803452 2803775 + hypothetical protein (NCBI ptt file) False
BC3033 BC3033 CDS None chromosome 2994090 2994980 - Transcriptional regulator, AraC family (NCBI ptt file) True
BC3477 BC3477 CDS None chromosome 3430469 3431434 + Quinone oxidoreductase (NCBI ptt file) False
BC3557 BC3557 CDS None chromosome 3528196 3530049 - Squalene--hopene cyclase (NCBI ptt file) False
BC3776 BC3776 CDS None chromosome 3748099 3748359 - Stage V sporulation protein S (NCBI ptt file) False
BC3801 BC3801 CDS None chromosome 3776449 3777351 - Dipicolinate synthase, A chain (NCBI ptt file) False
BC4281 BC4281 CDS None chromosome 4226271 4226525 + IG hypothetical 17696 (NCBI ptt file) False
BC4612 BC4612 CDS None chromosome 4559915 4560076 + hypothetical protein (NCBI ptt file) False
BC5099 BC5099 CDS None chromosome 5001545 5001733 - hypothetical protein (NCBI ptt file) False
BC5181 BC5181 CDS None chromosome 5078017 5078328 - hypothetical protein (NCBI ptt file) False
BC5222 BC5222 CDS None chromosome 5123464 5124348 + Transcriptional regulators, LysR family (NCBI ptt file) True
BC5410 BC5410 CDS None chromosome 5325069 5325695 - FMN-dependent NADH-azoreductase (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 76

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.