Organism : Bacillus cereus ATCC14579 | Module List:
Module 3 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 3

There are 21 regulatory influences for Module 3

Regulator Table (21)
Regulator Name Type
BC0742 tf
BC1003 tf
BC1134 tf
BC2442 tf
BC2936 tf
BC3690 tf
BC4859 tf
BC0980 tf
BC0848 tf
BC4703 tf
BC4652 tf
BC1915 tf
BC1131 tf
BC2558 tf
BC5176 tf
BC4902 tf
BC0840 tf
BC2386 tf
BC1884 tf
BC2217 tf
BC4256 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
3928 3.40e-01 aGGGgA.AGa
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3929 4.40e+01 GG.GGcccg
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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 3 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 0.00e+00 2.00e-06 14/22
Amino Acid Metabolism kegg subcategory 1.00e-06 3.00e-05 8/22
Histidine metabolism kegg pathway 0.00e+00 0.00e+00 6/22
Metabolism of Cofactors and Vitamins kegg subcategory 1.48e-04 1.57e-03 4/22
Thiamine metabolism kegg pathway 0.00e+00 0.00e+00 4/22
Membrane Transport kegg subcategory 9.06e-03 2.25e-02 3/22
ABC transporters kegg pathway 5.06e-03 1.52e-02 3/22
Global kegg category 1.00e-06 2.20e-05 12/22
Metabolism kegg subcategory 1.00e-06 2.20e-05 12/22
Metabolic pathways kegg pathway 2.00e-06 5.30e-05 11/22
Biosynthesis of secondary metabolites kegg pathway 1.80e-05 3.29e-04 7/22

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid biosynthesis tigr mainrole 0.00e+00 1.00e-06 5/22
Histidine family tigr sub1role 0.00e+00 0.00e+00 5/22
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 3.70e-05 8.80e-05 4/22
Thiamine tigr sub1role 0.00e+00 0.00e+00 4/22

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 0.00e+00 0.00e+00 19/22
Amino acid transport and metabolism cog subcategory 1.00e-06 3.00e-06 9/22
Coenzyme transport and metabolism cog subcategory 2.20e-05 7.50e-05 5/22
Inorganic ion transport and metabolism cog subcategory 1.14e-02 1.94e-02 3/22
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 3

There are 22 genes in Module 3

Gene Member Table (22)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0742 BC0742 CDS None chromosome 729477 730172 + Transcriptional activator tenA (NCBI ptt file) True
BC0743 BC0743 CDS None chromosome 730141 730890 + Hydroxymethylpyrimidine transport ATP-binding protein (NCBI ptt file) False
BC0744 BC0744 CDS None chromosome 730887 731642 + Hydroxymethylpyrimidine transport system permease protein (NCBI ptt file) False
BC0745 BC0745 CDS None chromosome 731624 732640 + Hydroxymethylpyrimidine-binding protein (NCBI ptt file) False
BC0746 BC0746 CDS None chromosome 732645 733271 + Regulatory protein TENI (NCBI ptt file) False
BC0747 BC0747 CDS None chromosome 733264 734373 + Glycine oxidase (NCBI ptt file) False
BC0748 BC0748 CDS None chromosome 734389 734592 + ThiS protein (NCBI ptt file) False
BC0749 BC0749 CDS None chromosome 734589 735365 + Thiazole biosynthesis protein thiG (NCBI ptt file) False
BC0750 BC0750 CDS None chromosome 735358 736377 + Molybdopterin biosynthesis MoeB protein (NCBI ptt file) False
BC0751 BC0751 CDS None chromosome 736393 737205 + Phosphomethylpyrimidine kinase (NCBI ptt file) False
BC0905 BC0905 CDS None chromosome 893175 894179 + Proline racemase (NCBI ptt file) False
BC0906 BC0906 CDS None chromosome 894343 895320 + Ornithine cyclodeaminase (NCBI ptt file) False
BC1405 BC1405 CDS None chromosome 1369088 1369723 + ATP phosphoribosyltransferase (NCBI ptt file) False
BC1406 BC1406 CDS None chromosome 1369735 1371024 + Histidinol dehydrogenase (NCBI ptt file) False
BC1408 BC1408 CDS None chromosome 1371609 1372238 + Amidotransferase hisH (NCBI ptt file) False
BC1409 BC1409 CDS None chromosome 1372211 1372930 + Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI ptt file) False
BC1411 BC1411 CDS None chromosome 1373679 1373984 + Phosphoribosyl-AMP cyclohydrolase (NCBI ptt file) False
BC1412 BC1412 CDS None chromosome 1373995 1374318 + Phosphoribosyl-ATP pyrophosphatase (NCBI ptt file) False
BC3167 BC3167 CDS None chromosome 3137321 3138160 - Xanthine dehydrogenase FAD-binding subunit (NCBI ptt file) False
BC3168 BC3168 CDS None chromosome 3138157 3140199 - Xanthine dehydrogenase molybdopterin-binding subunit (NCBI ptt file) False
BC3475 BC3475 CDS None chromosome 3428648 3429160 - hypothetical protein (NCBI ptt file) False
BC4699 BC4699 DUMMY None chromosome 0 0 + None 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 3

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.