Organism : Bacillus cereus ATCC14579 | Module List:
Module 83 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 83

There are 15 regulatory influences for Module 83

Regulator Table (15)
Regulator Name Type
BC4204 tf
BC0586 tf
BC1131 tf
BC1996 tf
BC2250 tf
BC0953 tf
BC4222 tf
BC1673 tf
BC4902 tf
BC2340 tf
BC5339 tf
BC3069 tf
BC2903 tf
BC0435 tf
BC0356 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
4084 3.80e+02 AgACgAtgtgtTaccgcGg
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4085 1.70e+03 gGgGGAa
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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 83 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 4.89e-04 3.68e-03 10/24
Amino Acid Metabolism kegg subcategory 0.00e+00 7.00e-06 9/24
Phenylalanine tyrosine and tryptophan biosynthesis kegg pathway 0.00e+00 0.00e+00 8/24
Global kegg category 1.14e-04 1.29e-03 10/24
Metabolism kegg subcategory 1.14e-04 1.29e-03 10/24
Metabolic pathways kegg pathway 2.49e-04 2.29e-03 9/24
Biosynthesis of secondary metabolites kegg pathway 4.00e-06 9.90e-05 8/24

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid biosynthesis tigr mainrole 1.00e-06 2.00e-06 5/24
Aromatic amino acid family tigr sub1role 0.00e+00 0.00e+00 5/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.13e-02 3.47e-02 10/24
Amino acid transport and metabolism cog subcategory 1.50e-05 5.80e-05 8/24
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 83

There are 24 genes in Module 83

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC1232 BC1232 CDS None chromosome 1207773 1209200 + Anthranilate synthase component I (NCBI ptt file) False
BC1233 BC1233 CDS None chromosome 1209197 1209784 + Anthranilate synthase component II (NCBI ptt file) False
BC1234 BC1234 CDS None chromosome 1209781 1210806 + Anthranilate phosphoribosyltransferase (NCBI ptt file) False
BC1235 BC1235 CDS None chromosome 1210808 1211569 + Indole-3-glycerol phosphate synthase (NCBI ptt file) False
BC1236 BC1236 CDS None chromosome 1211572 1212180 + N-(5'-phosphoribosyl)anthranilate isomerase (NCBI ptt file) False
BC1237 BC1237 CDS None chromosome 1212177 1213370 + Tryptophan synthase beta chain (NCBI ptt file) False
BC1238 BC1238 CDS None chromosome 1213374 1214150 + Tryptophan synthase alpha chain (NCBI ptt file) False
BC1517 BC1517 CDS None chromosome 1469795 1470880 + 3-dehydroquinate synthase (NCBI ptt file) False
BC1522 BC1522 CDS None chromosome 1475079 1475591 + Menaquinol-cytochrome c reductase iron-sulfur subunit (NCBI ptt file) False
BC1629 BC1629 CDS None chromosome 1586057 1587697 + Chemotaxis protein cheC (NCBI ptt file) False
BC1630 BC1630 CDS None chromosome 1587727 1589097 + hypothetical protein (NCBI ptt file) False
BC3063 BC3063 CDS None chromosome 3020743 3021390 - Pyrrolidone-carboxylate peptidase (NCBI ptt file) False
BC3065 BC3065 CDS None chromosome 3022371 3023075 - Permease (NCBI ptt file) False
BC4220 BC4220 CDS None chromosome 4170537 4171202 - ABC transporter permease protein (NCBI ptt file) False
BC4221 BC4221 CDS None chromosome 4171183 4172055 - ABC transporter ATP-binding protein (NCBI ptt file) False
BC4222 BC4222 CDS None chromosome 4172059 4172433 - Transcriptional regulator, GntR family (NCBI ptt file) True
BC4699 BC4699 DUMMY None chromosome 0 0 + None False
BC5079 BC5079 CDS None chromosome 4984927 4985697 - Short chain dehydrogenase (NCBI ptt file) False
BC5080 BC5080 CDS None chromosome 4985716 4986513 - Methyltransferase (NCBI ptt file) False
BC5081 BC5081 CDS None chromosome 4986506 4988074 - NADH oxidase (NOXASE) (NCBI ptt file) False
BC5082 BC5082 CDS None chromosome 4988049 4989026 - hypothetical protein (NCBI ptt file) False
BC5083 BC5083 CDS None chromosome 4989031 4990002 - Lantibiotic biosynthesis protein (NCBI ptt file) False
BC5084 BC5084 CDS None chromosome 4990018 4992633 - Lanthionine biosynthesis protein (NCBI ptt file) False
BC5085 BC5085 CDS None chromosome 4992661 4994304 - hypothetical Cytosolic 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 83

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.