Organism : Bacillus cereus ATCC14579 | Module List:
Module 311 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 311

There are 16 regulatory influences for Module 311

Regulator Table (16)
Regulator Name Type
BC0116 tf
BC1477 tf
BC2122 tf
BC0122 tf
BC4603 tf
BC1884 tf
BC2109 tf
BC3844 tf
BC5481 tf
BC4902 tf
BC0613 tf
BC3792 tf
BC5250 tf
BC0473 tf
BC3207 tf
BC3814 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
4536 6.00e-01 ATagaaaAgGAaggG
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4537 2.90e+03 GGaGGaGGaCTaGC
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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 311 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Cofactors and Vitamins kegg subcategory 1.19e-03 6.40e-03 3/20
Porphyrin and chlorophyll metabolism kegg pathway 1.00e-06 2.30e-05 3/20
Cellular Processes kegg category 0.00e+00 0.00e+00 7/20
Cell Motility kegg subcategory 0.00e+00 0.00e+00 7/20
Bacterial chemotaxis kegg pathway 3.00e-06 7.00e-05 3/20
Flagellar assembly kegg pathway 0.00e+00 0.00e+00 7/20
Global kegg category 1.23e-02 2.77e-02 6/20
Metabolism kegg subcategory 1.23e-02 2.77e-02 6/20
Metabolic pathways kegg pathway 6.86e-03 1.84e-02 6/20
Biosynthesis of secondary metabolites kegg pathway 2.55e-02 4.77e-02 3/20

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 4.01e-04 7.34e-04 3/20
Heme, porphyrin, and cobalamin tigr sub1role 0.00e+00 1.00e-06 3/20
Cell envelope tigr mainrole 4.20e-05 9.90e-05 3/20
Biosynthesis and degradation of murein sacculus and peptidoglycan tigr sub1role 4.00e-06 1.20e-05 3/20

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 2.60e-05 8.60e-05 9/20
Cell wall/membrane/envelope biogenesis cog subcategory 3.31e-03 6.07e-03 3/20
Cell motility cog subcategory 0.00e+00 0.00e+00 6/20
Intracellular trafficking, secretion, and vesicular transport cog subcategory 0.00e+00 0.00e+00 5/20
Coenzyme transport and metabolism cog subcategory 1.99e-03 3.77e-03 3/20
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 311

There are 20 genes in Module 311

Gene Member Table (20)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0258 BC0258 CDS None chromosome 232054 233418 + UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D- alanyl ligase (NCBI ptt file) False
BC0296 BC0296 CDS None chromosome 259858 261405 + GMP synthase [glutamine-hydrolyzing] (NCBI ptt file) False
BC0352 BC0352 CDS None chromosome 329361 330788 + Glutamyl-tRNA(Gln) amidotransferase subunit B (NCBI ptt file) False
BC1067 BC1067 CDS None chromosome 1050214 1052331 + Multimodular transpeptidase-transglycosylase PBP 2C (NCBI ptt file) False
BC1068 BC1068 CDS None chromosome 1052509 1053555 + Uroporphyrinogen decarboxylase (NCBI ptt file) False
BC1069 BC1069 CDS None chromosome 1053588 1054505 + Ferrochelatase (NCBI ptt file) False
BC1070 BC1070 CDS None chromosome 1054539 1055945 + Protoporphyrinogen oxidase (NCBI ptt file) False
BC1661 BC1661 CDS None chromosome 1614874 1615098 + Flagellar motor switch protein fliN (NCBI ptt file) False
BC1662 BC1662 CDS None chromosome 1615113 1616099 + Flagellar motor switch protein fliM (NCBI ptt file) False
BC1663 BC1663 CDS None chromosome 1616110 1616469 + Flagellar motor switch protein fliN (NCBI ptt file) False
BC1664 BC1664 CDS None chromosome 1616482 1616802 + Flagellar motor switch protein fliN (NCBI ptt file) False
BC1665 BC1665 CDS None chromosome 1616799 1617557 + Flagellar biosynthetic protein fliP (NCBI ptt file) False
BC1666 BC1666 CDS None chromosome 1617591 1617866 + Flagellar biosynthetic protein fliQ (NCBI ptt file) False
BC1667 BC1667 CDS None chromosome 1617882 1618643 + Flagellar biosynthetic protein fliR (NCBI ptt file) False
BC1668 BC1668 CDS None chromosome 1618654 1619700 + Flagellar biosynthetic protein flhB (NCBI ptt file) False
BC1985 BC1985 DUMMY None chromosome 0 0 + None False
BC3844 BC3844 CDS None chromosome 3820824 3821156 - Signal recognition particle associated protein (NCBI ptt file) True
BC4050 BC4050 CDS None chromosome 4021891 4023954 - PTS system, glucose-specific IIABC component (NCBI ptt file) False
BC4738 BC4738 CDS None chromosome 4673234 4674427 - Multidrug resistance protein B (NCBI ptt file) False
BC5375 BC5375 CDS None chromosome 5291887 5293938 + Multimodular transpeptidase-transglycosylase PBP 2D (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 311

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.