Organism : Bacillus cereus ATCC14579 | Module List:
Module 202 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 202

There are 19 regulatory influences for Module 202

Regulator Table (19)
Regulator Name Type
BC1673 tf
BC0405 tf
BC3207 tf
BC4222 tf
BC1756 tf
BC1603 tf
BC4474 tf
BC1884 tf
BC3690 tf
BC4256 tf
BC1131 tf
BC5363 tf
BC3758 tf
BC0356 tf
BC3693 tf
BC3389 tf
BC0518 tf
BC5481 tf
BC2904 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
4320 2.30e-02 AGGaGg
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4321 3.50e+02 GcAAG.aGaACa
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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 202 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 4.33e-03 1.37e-02 9/26
Carbohydrate Metabolism kegg subcategory 1.67e-02 3.49e-02 3/26
Metabolism of Cofactors and Vitamins kegg subcategory 3.42e-04 2.88e-03 4/26
Biotin metabolism kegg pathway 0.00e+00 0.00e+00 4/26
Global kegg category 1.27e-03 6.61e-03 9/26
Metabolism kegg subcategory 1.27e-03 6.61e-03 9/26
Metabolic pathways kegg pathway 2.42e-03 9.65e-03 8/26
Biosynthesis of secondary metabolites kegg pathway 1.51e-02 3.23e-02 4/26
Microbial metabolism in diverse environments kegg pathway 1.96e-02 3.91e-02 3/26

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 8.80e-05 1.88e-04 4/26
Biotin tigr sub1role 0.00e+00 0.00e+00 4/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell wall/membrane/envelope biogenesis cog subcategory 8.79e-03 1.52e-02 3/26
Coenzyme transport and metabolism cog subcategory 6.20e-05 1.72e-04 5/26
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 202

There are 26 genes in Module 202

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0746 BC0746 CDS None chromosome 732645 733271 + Regulatory protein TENI (NCBI ptt file) False
BC0990 BC0990 CDS None chromosome 975839 976003 - hypothetical protein (NCBI ptt file) False
BC1878 BC1878 CDS None chromosome 1828970 1829152 + Phage protein (NCBI ptt file) False
BC2031 BC2031 CDS None chromosome 1974658 1975734 + Spore coat protein H (NCBI ptt file) False
BC2086 BC2086 CDS None chromosome 2031969 2032463 + hypothetical protein (NCBI ptt file) False
BC2159 BC2159 DUMMY None chromosome 0 0 + None False
BC2385 BC2385 CDS None chromosome 2329209 2330519 + Dehydrogenase (NCBI ptt file) False
BC2484 BC2484 CDS None chromosome 2453061 2454398 + Propionyl-CoA carboxylase biotin-containing subunit (NCBI ptt file) False
BC2832 BC2832 CDS None chromosome 2795984 2797468 - Aldehyde dehydrogenase (NCBI ptt file) False
BC2833 BC2833 CDS None chromosome 2797486 2798382 - Dihydrodipicolinate synthase (NCBI ptt file) False
BC3217 BC3217 CDS None chromosome 3197789 3199021 - putative phosphohydrolases, Icc family (NCBI ptt file) False
BC3336 BC3336 CDS None chromosome 3298826 3299665 - hypothetical protein (NCBI ptt file) False
BC3337 BC3337 CDS None chromosome 3299717 3300439 - Acetyltransferase (NCBI ptt file) False
BC3427 BC3427 CDS None chromosome 3391047 3391808 - Glycosyltransferase (NCBI ptt file) False
BC3691 BC3691 CDS None chromosome 3657765 3658568 - hypothetical protein (NCBI ptt file) False
BC3692 BC3692 CDS None chromosome 3658569 3659111 - hypothetical protein (NCBI ptt file) False
BC4114 BC4114 CDS None chromosome 4077281 4078279 - Biotin synthase (NCBI ptt file) False
BC4116 BC4116 CDS None chromosome 4079056 4079796 - BioH protein (NCBI ptt file) False
BC4117 BC4117 CDS None chromosome 4079793 4080980 - 8-amino-7-oxononanoate synthase (NCBI ptt file) False
BC4118 BC4118 CDS None chromosome 4080946 4081674 - Dethiobiotin synthetase (NCBI ptt file) False
BC4119 BC4119 CDS None chromosome 4081674 4083062 - Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file) False
BC4318 BC4318 CDS None chromosome 4261456 4261821 - hypothetical protein (NCBI ptt file) False
BC4319 BC4319 CDS None chromosome 4261818 4262921 - Spore protease (NCBI ptt file) False
BC4930 BC4930 CDS None chromosome 4850360 4851247 - Transcriptional regulator, DeoR family (NCBI ptt file) True
BC5202 BC5202 CDS None chromosome 5101249 5102574 - UDP-glucose 6-dehydrogenase (NCBI ptt file) False
BC5412 BC5412 CDS None chromosome 5326555 5328126 - Two-component sensor protein yhcY (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 202

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.