Organism : Bacillus cereus ATCC14579 | Module List:
Module 263 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 263

There are 10 regulatory influences for Module 263

Regulator Table (10)
Regulator Name Type
BC1489 tf
BC1059 tf
BC3497 tf
BC5340 tf
BC1987 tf
BC2351 tf
BC4930 tf
BC2794 tf
BC1531 tf
BC2401 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
4442 8.90e+02 aGGaggGAA
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4443 2.20e+03 ATTtCGcCG.aTgAtTCccc
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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 263 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.93e-02 3.16e-02 8/36
Carbohydrate transport and metabolism cog subcategory 1.62e-02 2.69e-02 4/36
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 263

There are 36 genes in Module 263

Gene Member Table (36)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0035 BC0035 CDS None chromosome 34380 35801 + Arginine decarboxylase (NCBI ptt file) False
BC0189 BC0189 CDS None chromosome 163304 163510 + hypothetical protein (NCBI ptt file) False
BC0254 BC0254 CDS None chromosome 226466 227638 + Homogentisate 1,2-dioxygenase (NCBI ptt file) False
BC0312 BC0312 CDS None chromosome 282045 282989 + UDP-glucose 4-epimerase (NCBI ptt file) False
BC0391 BC0391 CDS None chromosome 369985 370653 + hypothetical protein (NCBI ptt file) False
BC0664 BC0664 DUMMY None chromosome 0 0 + None False
BC0876 BC0876 CDS None chromosome 853895 854143 + hypothetical protein (NCBI ptt file) False
BC1050 BC1050 CDS None chromosome 1029203 1029946 + ABC-type transporter ATP-binding protein ecsA (NCBI ptt file) False
BC1132 BC1132 CDS None chromosome 1113612 1113815 - hypothetical protein (NCBI ptt file) False
BC1140 BC1140 CDS None chromosome 1124649 1124870 - Spore germination protein PF (NCBI ptt file) False
BC1144 BC1144 CDS None chromosome 1126193 1126399 - Spore germination protein PB (NCBI ptt file) False
BC1145 BC1145 CDS None chromosome 1126414 1126635 - Spore germination protein PA (NCBI ptt file) False
BC1176 BC1176 CDS None chromosome 1155369 1156115 + hypothetical protein (NCBI ptt file) False
BC1478 BC1478 CDS None chromosome 1435289 1437064 + Sensor protein resE (NCBI ptt file) False
BC1556 BC1556 CDS None chromosome 1504781 1505029 + hypothetical protein (NCBI ptt file) False
BC1772 BC1772 CDS None chromosome 1724627 1725514 + Beta-lactamase inhibitory protein II (NCBI ptt file) False
BC2037 BC2037 CDS None chromosome 1981013 1981882 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC2275 BC2275 CDS None chromosome 2217879 2218214 + hypothetical cytosolic protein pX02-70 (NCBI ptt file) False
BC2351 BC2351 CDS None chromosome 2298703 2299263 + Transcriptional regulator, MerR family (NCBI ptt file) True
BC2476 BC2476 CDS None chromosome 2446150 2446992 + phosphoesterase (NCBI ptt file) False
BC2507 BC2507 CDS None chromosome 2475653 2476495 - Transcriptional regulator, AraC family (NCBI ptt file) True
BC2604 BC2604 CDS None chromosome 2569292 2569708 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC2673 BC2673 CDS None chromosome 2657202 2658500 + Tetracycline resistance determinant tetV (NCBI ptt file) False
BC2687 BC2687 CDS None chromosome 2670595 2670876 + hypothetical protein (NCBI ptt file) False
BC3560 BC3560 CDS None chromosome 3531688 3531936 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC3622 BC3622 CDS None chromosome 3595034 3596272 - Multidrug resistance protein B (NCBI ptt file) False
BC3720 BC3720 CDS None chromosome 3685088 3685840 - Fructose repressor (NCBI ptt file) True
BC3897 BC3897 CDS None chromosome 3879156 3879923 - RNA binding protein (NCBI ptt file) False
BC4236 BC4236 CDS None chromosome 4184556 4185011 - ComG operon protein 4 (NCBI ptt file) False
BC4416 BC4416 CDS None chromosome 4357135 4358079 + Ferrichrome-binding protein (NCBI ptt file) False
BC4572 BC4572 CDS None chromosome 4517869 4518360 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC4809 BC4809 CDS None chromosome 4733728 4735581 - Two component system histidine kinase (NCBI ptt file) False
BC4810 BC4810 CDS None chromosome 4735578 4736267 - Two-component response regulator (NCBI ptt file) False
BC4819 BC4819 CDS None chromosome 4741527 4742474 + hypothetical protein (NCBI ptt file) False
BC5216 BC5216 CDS None chromosome 5116481 5117491 - PTS system, lichenan oligosaccharide-specific IIC component (NCBI ptt file) False
BC5448 BC5448 CDS None chromosome 5372599 5373615 - UDP-glucose 4-epimerase (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 263

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.