Organism : Bacillus cereus ATCC14579 | Module List:
Module 218 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 218

There are 9 regulatory influences for Module 218

Regulator Table (9)
Regulator Name Type
BC2632 tf
BC2979 tf
BC3493 tf
BC4010 tf
BC1032 tf
BC1427 tf
BC5097 tf
BC1490 tf
BC0954 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
4352 9.70e-05 agagaGG.Gata.aa
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4353 2.00e+04 CCATCGcccCTTGC
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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 218 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 2.37e-02 4.50e-02 10/37
Glyoxylate and dicarboxylate metabolism kegg pathway 1.40e-05 2.70e-04 3/37
Energy Metabolism kegg subcategory 1.84e-02 3.73e-02 3/37
Amino Acid Metabolism kegg subcategory 1.34e-02 2.97e-02 5/37

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 1.59e-03 2.48e-03 4/37

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 3.98e-03 7.23e-03 12/37
General function prediction only cog subcategory 1.64e-02 2.73e-02 7/37
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 218

There are 37 genes in Module 218

Gene Member Table (37)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0374 BC0374 CDS None chromosome 355507 356622 + Amidohydrolase amhX (NCBI ptt file) False
BC0398 BC0398 CDS None chromosome 377157 378467 - Benzoate transport protein (NCBI ptt file) False
BC0582 BC0582 CDS None chromosome 567859 568785 - Transporter, Drug/Metabolite Exporter family (NCBI ptt file) False
BC0590 BC0590 CDS None chromosome 578792 579274 + hypothetical protein (NCBI ptt file) False
BC0827 BC0827 CDS None chromosome 809589 809870 + hypothetical protein (NCBI ptt file) False
BC0829 BC0829 CDS None chromosome 810600 810968 + hypothetical protein (NCBI ptt file) False
BC1127 BC1127 CDS None chromosome 1108649 1110211 + Malate synthase (NCBI ptt file) False
BC1128 BC1128 CDS None chromosome 1110235 1111512 + Isocitrate lyase (NCBI ptt file) False
BC1202 BC1202 CDS None chromosome 1182712 1183452 - Serine/threonine protein phosphatase (NCBI ptt file) False
BC1340 BC1340 CDS None chromosome 1317544 1318608 - Sporulation kinase (NCBI ptt file) False
BC1675 BC1675 CDS None chromosome 1626333 1626644 + Branched-chain amino acid transport protein azlD (NCBI ptt file) False
BC2013 BC2013 CDS None chromosome 1958280 1959224 + Alpha/beta hydrolase (NCBI ptt file) False
BC2042 BC2042 CDS None chromosome 1985078 1985686 + putative NAD-dependent dehydrogenase (NCBI ptt file) False
BC2217 BC2217 CDS None chromosome 2161322 2161963 + Two-component response regulator yhcZ (NCBI ptt file) True
BC2281 BC2281 CDS None chromosome 2222161 2224653 + Multimodular transpeptidase-transglycosylase PBP 1A (NCBI ptt file) False
BC2395 BC2395 CDS None chromosome 2339566 2339832 + hypothetical protein (NCBI ptt file) False
BC2663 BC2663 DUMMY None chromosome 0 0 + None False
BC2757 BC2757 CDS None chromosome 2734567 2735415 - Tryptophan 2,3-dioxygenase (NCBI ptt file) False
BC2759 BC2759 CDS None chromosome 2736071 2737357 - L-kynurenine hydrolase (NCBI ptt file) False
BC2838 BC2838 CDS None chromosome 2803452 2803775 + hypothetical protein (NCBI ptt file) False
BC2899 BC2899 CDS None chromosome 2857955 2858464 - 2'-5' RNA ligase (NCBI ptt file) False
BC3022 BC3022 CDS None chromosome 2985169 2985444 - hypothetical protein (NCBI ptt file) False
BC3124 BC3124 CDS None chromosome 3094142 3094786 + Isochorismatase family (NCBI ptt file) False
BC3162 BC3162 CDS None chromosome 3132717 3133907 - Bicyclomycin resistance protein (NCBI ptt file) False
BC3248 BC3248 CDS None chromosome 3227466 3228638 - D-3-phosphoglycerate dehydrogenase (NCBI ptt file) False
BC3594 BC3594 CDS None chromosome 3570432 3570875 + PhnB protein (NCBI ptt file) False
BC3656 BC3656 CDS None chromosome 3626385 3626846 + Methyltransferase (NCBI ptt file) False
BC3657 BC3657 CDS None chromosome 3626850 3627422 - 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme (NCBI ptt file) False
BC3939 BC3939 CDS None chromosome 3918193 3919191 - Amidase (NCBI ptt file) False
BC3993 BC3993 CDS None chromosome 3966995 3969103 - Polyphosphate kinase (NCBI ptt file) False
BC4003 BC4003 CDS None chromosome 3977392 3979680 + 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (NCBI ptt file) False
BC4042 BC4042 CDS None chromosome 4014323 4015201 - 3-hydroxyisobutyrate dehydrogenase (NCBI ptt file) False
BC4082 BC4082 CDS None chromosome 4050157 4050828 + hypothetical protein (NCBI ptt file) False
BC4598 BC4598 CDS None chromosome 4544640 4545029 - FxsA protein (NCBI ptt file) False
BC4668 BC4668 CDS None chromosome 4609551 4610477 + Virulence factor mviM (NCBI ptt file) False
BC4767 BC4767 CDS None chromosome 4700507 4700683 + hypothetical protein (NCBI ptt file) False
BC5366 BC5366 CDS None chromosome 5284155 5285141 + Muramoyltetrapeptide carboxypeptidase (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 218

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.