Organism : Bacillus cereus ATCC14579 | Module List:
Module 137 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 137

There are 12 regulatory influences for Module 137

Regulator Table (12)
Regulator Name Type
BC3493 tf
BC0114 tf
BC0598 tf
BC2632 tf
BC3826 tf
BC0613 tf
BC1622 tf
BC2362 tf
BC1841 tf
BC4057 tf
BC0954 tf
BC0856 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
4190 1.10e-11 tAGggGgaacaa
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4191 2.80e-04 atAtgttAgAAtatTtAGAaaA
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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 137 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 4.69e-03 1.45e-02 5/30
Environmental Information Processing kegg category 4.61e-03 1.43e-02 5/30
Membrane Transport kegg subcategory 8.31e-04 5.11e-03 5/30
ABC transporters kegg pathway 3.43e-04 2.89e-03 5/30
Biosynthesis of secondary metabolites kegg pathway 2.72e-02 4.99e-02 4/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 4.99e-03 6.82e-03 3/30
Amino acids and amines tigr sub1role 1.20e-05 3.40e-05 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.15e-02 3.51e-02 12/30
Amino acid transport and metabolism cog subcategory 0.00e+00 1.00e-06 11/30
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 137

There are 30 genes in Module 137

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0012 BC0012 CDS None chromosome 14232 15233 - IG hypothetical 16768 (NCBI ptt file) False
BC0013 BC0013 CDS None chromosome 15349 16812 + Inosine-5'-monophosphate dehydrogenase (NCBI ptt file) False
BC0114 BC0114 CDS None chromosome 108500 109159 + RNA polymerase sigma-H factor (NCBI ptt file) True
BC0215 BC0215 CDS None chromosome 190691 192331 - Oligopeptide-binding protein oppA (NCBI ptt file) False
BC0859 BC0859 CDS None chromosome 833052 834791 - Oligopeptide-binding protein oppA (NCBI ptt file) False
BC1149 BC1149 CDS None chromosome 1128487 1129677 - Ornithine aminotransferase (NCBI ptt file) False
BC1180 BC1180 CDS None chromosome 1160334 1161272 + Oligopeptide transport system permease protein oppB (NCBI ptt file) False
BC1181 BC1181 CDS None chromosome 1161269 1162285 + Oligopeptide transport system permease protein oppC (NCBI ptt file) False
BC1182 BC1182 CDS None chromosome 1162304 1163347 + Oligopeptide transport ATP-binding protein oppD (NCBI ptt file) False
BC1183 BC1183 CDS None chromosome 1163340 1164275 + Oligopeptide transport ATP-binding protein oppF (NCBI ptt file) False
BC1366 BC1366 CDS None chromosome 1335277 1335675 + SSEB protein (NCBI ptt file) False
BC1396 BC1396 CDS None chromosome 1358466 1359362 + Branched-chain amino acid aminotransferase (NCBI ptt file) False
BC1799 BC1799 CDS None chromosome 1753240 1753770 - Ribosomal-protein-alanine acetyltransferase (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
BC2094 BC2094 CDS None chromosome 2038877 2039662 - Acetyltransferase (NCBI ptt file) False
BC2142 BC2142 CDS None chromosome 2088806 2089081 + Stage V sporulation protein S (NCBI ptt file) False
BC2757 BC2757 CDS None chromosome 2734567 2735415 - Tryptophan 2,3-dioxygenase (NCBI ptt file) False
BC2758 BC2758 CDS None chromosome 2735439 2736068 - Metal-dependent hydrolase (NCBI ptt file) False
BC2759 BC2759 CDS None chromosome 2736071 2737357 - L-kynurenine hydrolase (NCBI ptt file) False
BC3494 BC3494 CDS None chromosome 3449789 3450298 + hypothetical protein (NCBI ptt file) False
BC3955 BC3955 CDS None chromosome 3935628 3935930 - hypothetical protein (NCBI ptt file) False
BC3968 BC3968 CDS None chromosome 3944446 3944838 + hypothetical protein (NCBI ptt file) False
BC4133 BC4133 CDS None chromosome 4097041 4097994 - Zinc metallohydrolase (NCBI ptt file) False
BC4427 BC4427 CDS None chromosome 4368559 4369410 - Prephenate dehydratase (NCBI ptt file) False
BC4682 BC4682 CDS None chromosome 4618873 4619364 - IAA acetyltransferase (NCBI ptt file) False
BC4683 BC4683 CDS None chromosome 4619361 4619909 - Ribosomal-protein-serine acetyltransferase (NCBI ptt file) False
BC5076 BC5076 CDS None chromosome 4983112 4983894 - Short chain dehydrogenase (NCBI ptt file) False
BC5077 BC5077 CDS None chromosome 4983851 4984330 - hypothetical protein (NCBI ptt file) False
BC5453 BC5453 CDS None chromosome 5378253 5380070 + Oligoendopeptidase 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 137

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.