Organism : Bacillus cereus ATCC14579 | Module List:
Module 63 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 63

There are 9 regulatory influences for Module 63

Regulator Table (9)
Regulator Name Type
BC2794 tf
BC3497 tf
BC0758 tf
BC3244 tf
BC0649 tf
BC3493 tf
BC2444 tf
BC3160 tf
BC0950 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
4046 1.20e+04 GaGgaggA
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4047 1.90e+04 CAGCGCCc
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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 63 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 2.40e-03 4.49e-03 10/37
Signal transduction mechanisms cog subcategory 8.27e-03 1.44e-02 4/37
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 63

There are 37 genes in Module 63

Gene Member Table (37)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0013 BC0013 CDS None chromosome 15349 16812 + Inosine-5'-monophosphate dehydrogenase (NCBI ptt file) False
BC0565 BC0565 CDS None chromosome 548377 549126 + Ankyrin (NCBI ptt file) False
BC0572 BC0572 CDS None chromosome 555714 556412 + Two-component response regulator (NCBI ptt file) False
BC0649 BC0649 CDS None chromosome 644180 645133 - Transcriptional regulator, DeoR family (NCBI ptt file) True
BC0766 BC0766 CDS None chromosome 751478 752473 - Methylthioribose transport system permease protein (NCBI ptt file) False
BC1097 BC1097 CDS None chromosome 1081485 1081703 + hypothetical protein (NCBI ptt file) False
BC1258 BC1258 CDS None chromosome 1234921 1235337 + hypothetical protein (NCBI ptt file) False
BC1774 BC1774 CDS None chromosome 1726104 1726640 - Peptide methionine sulfoxide reductase (NCBI ptt file) False
BC1840 BC1840 CDS None chromosome 1799885 1800790 - Transporter, Drug/Metabolite Exporter family (NCBI ptt file) False
BC1912 BC1912 CDS None chromosome 1857320 1858936 - Phage protein (NCBI ptt file) False
BC1913 BC1913 CDS None chromosome 1859009 1859335 - Phage protein (NCBI ptt file) False
BC1914 BC1914 CDS None chromosome 1859412 1859651 - Phage protein (NCBI ptt file) False
BC2315 BC2315 CDS None chromosome 2262815 2263339 + DinB protein (NCBI ptt file) False
BC2428 BC2428 CDS None chromosome 2372641 2373123 - hypothetical protein (NCBI ptt file) False
BC2539 BC2539 CDS None chromosome 2511862 2512845 + Two-component sensor kinase yxdK (NCBI ptt file) False
BC2603 BC2603 CDS None chromosome 2568385 2569149 + hypothetical protein (NCBI ptt file) False
BC2740 BC2740 CDS None chromosome 2719337 2720641 + Protein translocase subunit SecY (NCBI ptt file) False
BC2794 BC2794 CDS None chromosome 2762249 2762935 - RNA polymerase ECF-type sigma factor (NCBI ptt file) True
BC3148 BC3148 CDS None chromosome 3118161 3118721 + Streptothricin acetyltransferase (NCBI ptt file) False
BC3497 BC3497 CDS None chromosome 3453804 3454148 + Transcriptional regulator, ArsR family (NCBI ptt file) True
BC3498 BC3498 CDS None chromosome 3454176 3455165 + Quinone oxidoreductase (NCBI ptt file) False
BC3584 BC3584 CDS None chromosome 3557857 3559527 - Oligopeptide-binding protein oppA (NCBI ptt file) False
BC3645 BC3645 CDS None chromosome 3615042 3615530 - CcdC protein (NCBI ptt file) False
BC3747 BC3747 CDS None chromosome 3710553 3713282 + Sensory box/GGDEF family protein (NCBI ptt file) False
BC3876 BC3876 CDS None chromosome 3857965 3858489 + hypothetical protein (NCBI ptt file) False
BC4014 BC4014 CDS None chromosome 3989779 3991539 + Neopullulanase (NCBI ptt file) False
BC4131 BC4131 CDS None chromosome 4096018 4096206 + hypothetical protein (NCBI ptt file) False
BC4146 BC4146 CDS None chromosome 4111747 4112307 - Protein erfK/srfK precursor (NCBI ptt file) False
BC4147 BC4147 CDS None chromosome 4112324 4113292 - Integral membrane protein (NCBI ptt file) False
BC4305 BC4305 CDS None chromosome 4247773 4248399 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC4464 BC4464 CDS None chromosome 4407885 4409186 - Folylpolyglutamate synthase (NCBI ptt file) False
BC4514 BC4514 CDS None chromosome 4458868 4459647 + D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) False
BC4666 BC4666 CDS None chromosome 4607187 4608641 - Two component system histidine kinase (NCBI ptt file) False
BC4839 BC4839 CDS None chromosome 4761046 4761798 + ABC transporter ATP-binding protein (NCBI ptt file) False
BC4946 BC4946 CDS None chromosome 4863082 4863552 + hypothetical protein (NCBI ptt file) False
BC4947 BC4947 CDS None chromosome 4863533 4864177 + hypothetical protein (NCBI ptt file) False
BC5068 BC5068 CDS None chromosome 4976198 4976554 + CrcB family 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 63

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.