Organism : Bacillus cereus ATCC14579 | Module List:
Module 475 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 475

There are 8 regulatory influences for Module 475

Regulator Table (8)
Regulator Name Type
BC5143 tf
BC5481 tf
BC2434 tf
BC5038 tf
BC0405 tf
BC1936 tf
BC2815 tf
BC4670 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
4860 1.50e+00 AaaGGgGA
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4861 2.30e+04 ggtAgaTTaaaAgggaAaGg
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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 475 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 7.11e-03 1.89e-02 4/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 9.45e-03 1.63e-02 10/32
General function prediction only cog subcategory 1.69e-03 3.24e-03 8/32
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 475

There are 32 genes in Module 475

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0168 BC0168 CDS None chromosome 147036 148103 + Mrp protein (NCBI ptt file) False
BC0236 BC0236 CDS None chromosome 211116 211649 + Transglycosylase (NCBI ptt file) False
BC0290 BC0290 CDS None chromosome 253404 255338 - ABC transporter ATP-binding protein uup (NCBI ptt file) False
BC0498 BC0498 CDS None chromosome 488822 489634 + Regulatory protein recX (NCBI ptt file) True
BC0499 BC0499 CDS None chromosome 489645 489962 + Transcriptional regulator (NCBI ptt file) True
BC0589 BC0589 CDS None chromosome 575843 578779 + Formate dehydrogenase alpha chain (NCBI ptt file) False
BC0595 BC0595 CDS None chromosome 584652 585029 + Cadmium efflux system accessory protein (NCBI ptt file) True
BC0596 BC0596 CDS None chromosome 585053 587419 + Zinc-transporting ATPase (NCBI ptt file) False
BC0630 BC0630 CDS None chromosome 625300 626010 + Trehalose operon transcriptional repressor (NCBI ptt file) True
BC1163 BC1163 CDS None chromosome 1143534 1144415 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC1689 BC1689 CDS None chromosome 1639475 1639636 + hypothetical protein (NCBI ptt file) False
BC1711 BC1711 CDS None chromosome 1659535 1660245 - Short chain dehydrogenase (NCBI ptt file) False
BC2437 BC2437 CDS None chromosome 2380112 2380288 + hypothetical protein (NCBI ptt file) False
BC2843 BC2843 CDS None chromosome 2806365 2807129 + hypothetical protein (NCBI ptt file) False
BC3438 BC3438 CDS None chromosome 3399142 3399462 - Transcriptional regulator, PadR family (NCBI ptt file) True
BC3602 BC3602 CDS None chromosome 3579585 3580037 - Anaerobic ribonucleoside-triphosphate reductase activating protein (NCBI ptt file) False
BC3616 BC3616 CDS None chromosome 3589995 3592718 - Aconitate hydratase (NCBI ptt file) False
BC3755 BC3755 CDS None chromosome 3719737 3720093 - Murein hydrolase exporter (NCBI ptt file) False
BC3757 BC3757 CDS None chromosome 3721747 3721938 - hypothetical protein (NCBI ptt file) False
BC3990 BC3990 CDS None chromosome 3964645 3965415 - 2,4-dienoyl-CoA reductase [NADPH] (NCBI ptt file) False
BC4086 BC4086 CDS None chromosome 4054620 4055213 - Purine nucleoside phosphorylase (NCBI ptt file) False
BC4087 BC4087 CDS None chromosome 4055455 4056639 - Phosphopentomutase (NCBI ptt file) False
BC4380 BC4380 CDS None chromosome 4319560 4319838 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC4424 BC4424 CDS None chromosome 4365987 4367129 + Cysteine desulfhydrase (NCBI ptt file) False
BC4583 BC4583 CDS None chromosome 4527960 4528988 - NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file) False
BC4658 BC4658 CDS None chromosome 4600018 4600578 - Maltose O-acetyltransferase (NCBI ptt file) False
BC4964 BC4964 CDS None chromosome 4874769 4874981 + hypothetical protein (NCBI ptt file) False
BC5172 BC5172 CDS None chromosome 5070635 5070862 - hypothetical protein (NCBI ptt file) False
BC5336 BC5336 CDS None chromosome 5243592 5243960 - Sporulation initiation phosphotransferase F (NCBI ptt file) False
BC5379 BC5379 CDS None chromosome 5295520 5296824 - dGTP triphosphohydrolase (NCBI ptt file) False
BC5385 BC5385 CDS None chromosome 5301817 5302509 + Prespore specific transcriptional activator rsfA (NCBI ptt file) True
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.

Comments for Module 475

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.