Organism : Bacillus cereus ATCC14579 | Module List:
Module 434 Profile

GeneModule member RegulatorRegulator MotifMotif
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 434

There are 10 regulatory influences for Module 434

Regulator Table (10)
Regulator Name Type
BC3653 tf
BC5481 tf
BC0598 tf
BC3740 tf
BC2632 tf
BC2770 tf
BC3982 tf
BC4525 tf
BC4104 tf
BC4652 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
4778 1.10e+01 GCaTCCCC
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4779 2.70e+03 GGGGTGAGGG
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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 434 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Environmental Information Processing kegg category 4.28e-04 3.38e-03 6/27
Membrane Transport kegg subcategory 1.87e-02 3.78e-02 3/27
ABC transporters kegg pathway 1.07e-02 2.52e-02 3/27
Signal Transduction kegg subcategory 7.62e-04 4.86e-03 3/27
Two-component system kegg pathway 7.62e-04 4.86e-03 3/27

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 434

There are 27 genes in Module 434

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0251 BC0251 CDS None chromosome 223846 223965 + hypothetical protein (NCBI ptt file) False
BC0699 BC0699 CDS None chromosome 698715 700130 - Arginine permease (NCBI ptt file) False
BC1181 BC1181 CDS None chromosome 1161269 1162285 + Oligopeptide transport system permease protein oppC (NCBI ptt file) False
BC1183 BC1183 CDS None chromosome 1163340 1164275 + Oligopeptide transport ATP-binding protein oppF (NCBI ptt file) False
BC1340 BC1340 CDS None chromosome 1317544 1318608 - Sporulation kinase (NCBI ptt file) False
BC1927 BC1927 CDS None chromosome 1872219 1873436 + Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein (NCBI ptt file) False
BC1933 BC1933 CDS None chromosome 1877835 1878383 + hypothetical protein (NCBI ptt file) False
BC2062 BC2062 CDS None chromosome 2003743 2004204 - hypothetical protein (NCBI ptt file) False
BC2186 BC2186 CDS None chromosome 2133477 2134064 + hypothetical protein (NCBI ptt file) False
BC2632 BC2632 CDS None chromosome 2598172 2599017 + Transcriptional regulator, AraC family (NCBI ptt file) True
BC2633 BC2633 CDS None chromosome 2599618 2599812 + hypothetical protein (NCBI ptt file) False
BC2676 BC2676 CDS None chromosome 2660602 2661480 + Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) False
BC2729 BC2729 CDS None chromosome 2704132 2705172 - Penicillin-binding protein (NCBI ptt file) False
BC2767 BC2767 CDS None chromosome 2742855 2742968 - hypothetical Membrane Associated Protein (NCBI ptt file) False
BC2787 BC2787 CDS None chromosome 2757272 2757784 - HIT family hydrolase (NCBI ptt file) False
BC2814 BC2814 CDS None chromosome 2779905 2780285 - Butirosin biosynthesis protein BtrG (NCBI ptt file) False
BC3367 BC3367 CDS None chromosome 3329013 3329189 + hypothetical protein (NCBI ptt file) False
BC3755 BC3755 CDS None chromosome 3719737 3720093 - Murein hydrolase exporter (NCBI ptt file) False
BC3990 BC3990 CDS None chromosome 3964645 3965415 - 2,4-dienoyl-CoA reductase [NADPH] (NCBI ptt file) False
BC4166 BC4166 CDS None chromosome 4130210 4130443 + IG hypothetical 17391 (NCBI ptt file) False
BC4448 BC4448 CDS None chromosome 4386875 4388224 + hypothetical protein (NCBI ptt file) False
BC4522 BC4522 DUMMY None chromosome 0 0 + None False
BC4938 BC4938 CDS None chromosome 4856215 4857285 + NADH dehydrogenase (NCBI ptt file) False
BC4964 BC4964 CDS None chromosome 4874769 4874981 + hypothetical protein (NCBI ptt file) False
BC5009 BC5009 CDS None chromosome 4913172 4915181 - Methyl-accepting chemotaxis protein (NCBI ptt file) False
BC5438 BC5438 CDS None chromosome 5361187 5361879 - Murein hydrolase export regulator (NCBI ptt file) False
BC5482 BC5482 CDS None chromosome 5403316 5404077 - Sporulation initiation inhibitor protein soj (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.

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.