Organism : Bacillus cereus ATCC14579 | Module List:
Module 25 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 25

There are 14 regulatory influences for Module 25

Regulator Table (14)
Regulator Name Type
BC2680 tf
BC3903 tf
BC0647 tf
BC0954 tf
BC1884 tf
BC1850 tf
BC4053 tf
BC3084 tf
BC3069 tf
BC3434 tf
BC3175 tf
BC2386 tf
BC3589 tf
BC3033 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
3972 6.20e+02 aaag.aGgaA.acaa
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3973 8.30e+00 AAAGGAga
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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 25 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
sigma70-ECF tigrfam 1.00e-06 3.00e-06 3/37

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 25

There are 37 genes in Module 25

Gene Member Table (37)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0396 BC0396 CDS None chromosome 375140 376249 + ATPase (NCBI ptt file) False
BC0484 BC0484 CDS None chromosome 474290 474691 + hypothetical protein (NCBI ptt file) False
BC0627 BC0627 CDS None chromosome 620881 621234 + hypothetical protein (NCBI ptt file) False
BC0647 BC0647 CDS None chromosome 642203 642760 + RNA polymerase ECF-type sigma factor (NCBI ptt file) True
BC0783 BC0783 CDS None chromosome 767340 768425 - Spore germination protein, gerC family (NCBI ptt file) False
BC0810 BC0810 CDS None chromosome 794362 794640 + hypothetical protein (NCBI ptt file) False
BC0886 BC0886 CDS None chromosome 866218 867090 + hydrolase (HAD superfamily) (NCBI ptt file) False
BC1096 BC1096 CDS None chromosome 1081019 1081264 + hypothetical protein (NCBI ptt file) False
BC1189 BC1189 CDS None chromosome 1169136 1169810 - Integral membrane protein (NCBI ptt file) False
BC1205 BC1205 CDS None chromosome 1185868 1186620 - Methyltransferase (NCBI ptt file) False
BC1274 BC1274 CDS None chromosome 1252363 1252584 - hypothetical protein (NCBI ptt file) False
BC1480 BC1480 CDS None chromosome 1437867 1438481 + Cell wall endopeptidase, family M23/M37 (NCBI ptt file) False
BC1604 BC1604 CDS None chromosome 1562311 1563039 + hypothetical protein (NCBI ptt file) False
BC1691 BC1691 CDS None chromosome 1641022 1641597 + Phosphoglycerate mutase (NCBI ptt file) False
BC1731 BC1731 CDS None chromosome 1676198 1676536 - RNA polymerase ECF-type sigma factor (NCBI ptt file) True
BC1737 BC1737 CDS None chromosome 1682303 1683400 + Cardiolipin synthetase (NCBI ptt file) False
BC2162 BC2162 CDS None chromosome 2103971 2104852 + Methyltransferase (NCBI ptt file) False
BC2424 BC2424 CDS None chromosome 2366583 2367014 + hypothetical protein (NCBI ptt file) False
BC2543 BC2543 CDS None chromosome 2516758 2517528 + ABC transporter ATP-binding protein (NCBI ptt file) False
BC2551 BC2551 CDS None chromosome 2525985 2526674 + Transcriptional activator tenA (NCBI ptt file) True
BC2587 BC2587 CDS None chromosome 2552091 2553395 + Phage Prohead Protease (NCBI ptt file) False
BC2590 BC2590 CDS None chromosome 2553957 2554286 + Phage protein (NCBI ptt file) False
BC2593 BC2593 CDS None chromosome 2555322 2555708 + Phage protein (NCBI ptt file) False
BC2691 BC2691 CDS None chromosome 2674785 2675210 + Acetyltransferase (NCBI ptt file) False
BC2906 BC2906 CDS None chromosome 2861646 2862239 - hypothetical protein (NCBI ptt file) False
BC2986 BC2986 CDS None chromosome 2946536 2948179 - Alkaline phosphatase (NCBI ptt file) False
BC3198 BC3198 CDS None chromosome 3174238 3174567 - hypothetical protein (NCBI ptt file) False
BC3515 BC3515 CDS None chromosome 3469901 3471970 + hypothetical Glycosyltransferase (NCBI ptt file) False
BC3589 BC3589 CDS None chromosome 3566123 3566656 - RNA polymerase ECF-type sigma factor (NCBI ptt file) True
BC3620 BC3620 CDS None chromosome 3594346 3594480 + Spore coat protein L (NCBI ptt file) False
BC3879 BC3879 CDS None chromosome 3859436 3860821 + Transporter (NCBI ptt file) False
BC3997 BC3997 CDS None chromosome 3972696 3973349 - Diguanylate cyclase/phosphodiesterase domain 2 (EAL) (NCBI ptt file) False
BC4044 BC4044 CDS None chromosome 4016433 4017728 - Sensory box/GGDEF family protein (NCBI ptt file) False
BC4075 BC4075 CDS None chromosome 4044135 4045325 - D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) False
BC4228 BC4228 CDS None chromosome 4179457 4180254 + hypothetical protein (NCBI ptt file) False
BC4527 BC4527 CDS None chromosome 4471960 4472853 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC5030 BC5030 CDS None chromosome 4931736 4932638 + Transporter, Drug/Metabolite Exporter family (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 25

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.