Organism : Bacillus cereus ATCC14579 | Module List:
Module 387 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 387

There are 12 regulatory influences for Module 387

Regulator Table (12)
Regulator Name Type
BC1083 tf
BC2469 tf
BC2794 tf
BC4960 tf
BC0659 tf
BC4433 tf
BC0410 tf
BC4611 tf
BC0613 tf
BC4570 tf
BC4474 tf
BC1335 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
4684 3.00e-23 tAtGAAAaCGcTtaCa
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4685 5.90e-06 aggGtGGA
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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 387 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.00e-06 3.60e-05 15/29
Carbohydrate Metabolism kegg subcategory 0.00e+00 0.00e+00 10/29
Starch and sucrose metabolism kegg pathway 0.00e+00 0.00e+00 5/29
Environmental Information Processing kegg category 0.00e+00 5.00e-06 10/29
Membrane Transport kegg subcategory 0.00e+00 0.00e+00 10/29
Phosphotransferase system (PTS) kegg pathway 0.00e+00 0.00e+00 9/29
Global kegg category 1.12e-02 2.59e-02 8/29
Metabolism kegg subcategory 1.12e-02 2.59e-02 8/29
Metabolic pathways kegg pathway 5.56e-03 1.61e-02 8/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
EIIB_glc tigrfam 0.00e+00 0.00e+00 3/29
Signal transduction tigr mainrole 0.00e+00 0.00e+00 6/29
PTS tigr sub1role 0.00e+00 0.00e+00 6/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 5.00e-06 2.20e-05 18/29
Carbohydrate transport and metabolism cog subcategory 0.00e+00 0.00e+00 13/29
Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific cog 0.00e+00 0.00e+00 4/29
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 387

There are 29 genes in Module 387

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0338 BC0338 CDS None chromosome 314021 314176 + hypothetical protein (NCBI ptt file) False
BC0378 BC0378 CDS None chromosome 360193 361422 + 5-methylthioribose kinase (NCBI ptt file) False
BC0380 BC0380 CDS None chromosome 362532 363173 + L-fuculose phosphate aldolase (NCBI ptt file) False
BC0414 BC0414 CDS None chromosome 396736 398373 + PTS system, glucose-specific IIBC component (NCBI ptt file) False
BC0415 BC0415 CDS None chromosome 398378 399169 + Exodeoxyribonuclease III (NCBI ptt file) False
BC0592 BC0592 CDS None chromosome 581671 582804 + Alanine dehydrogenase (NCBI ptt file) False
BC0631 BC0631 CDS None chromosome 626152 627579 + PTS system, trehalose-specific IIBC component (NCBI ptt file) False
BC0632 BC0632 CDS None chromosome 627593 629254 + Trehalose-6-phosphate hydrolase (NCBI ptt file) False
BC0774 BC0774 CDS None chromosome 759841 761316 - Sucrose-6-phosphate hydrolase (NCBI ptt file) False
BC0775 BC0775 CDS None chromosome 761334 762710 - PTS system, sucrose-specific IIBC component (NCBI ptt file) False
BC0807 BC0807 CDS None chromosome 792365 792685 + PTS system, diacetylchitobiose-specific IIA component (NCBI ptt file) False
BC0808 BC0808 CDS None chromosome 792687 792992 + PTS system, diacetylchitobiose-specific IIB component (NCBI ptt file) False
BC0809 BC0809 CDS None chromosome 793073 794386 + PTS system, diacetylchitobiose-specific IIC component (NCBI ptt file) False
BC0841 BC0841 CDS None chromosome 819547 820431 + Glucokinase regulatory protein (NCBI ptt file) False
BC0842 BC0842 CDS None chromosome 820474 821820 + PTS system, sucrose-specific IIBC component (NCBI ptt file) False
BC0843 BC0843 CDS None chromosome 821869 822942 + outer surface protein (NCBI ptt file) False
BC1083 BC1083 CDS None chromosome 1069993 1070946 + Transcriptional regulator, LacI family (NCBI ptt file) True
BC1185 BC1185 CDS None chromosome 1166217 1167863 + Oligopeptide-binding protein oppA (NCBI ptt file) False
BC1440 BC1440 CDS None chromosome 1400345 1400608 + hypothetical protein (NCBI ptt file) False
BC2238 BC2238 CDS None chromosome 2186326 2186922 + hypothetical protein (NCBI ptt file) False
BC3718 BC3718 CDS None chromosome 3682310 3684166 - PTS system, fructose-specific IIABC component (NCBI ptt file) False
BC4526 BC4526 CDS None chromosome 4470085 4471602 - acyl-CoA synthase (RefSeq) False
BC4814 BC4814 CDS None chromosome 4738200 4738415 - hypothetical protein (NCBI ptt file) False
BC4843 BC4843 CDS None chromosome 4766285 4767310 - 2-dehydro-3-deoxygluconokinase (NCBI ptt file) False
BC4844 BC4844 CDS None chromosome 4767294 4768049 - 4-Hydroxy-2-oxoglutarate aldolase (NCBI ptt file) False
BC4845 BC4845 CDS None chromosome 4768051 4769154 - L-seryl-tRNA(Sec) selenium transferase (NCBI ptt file) False
BC4846 BC4846 CDS None chromosome 4769132 4770232 - Dihydroorotase (NCBI ptt file) False
BC5211 BC5211 CDS None chromosome 5112456 5113763 - PTS system, lichenan oligosaccharide-specific IIC component (NCBI ptt file) False
BC5228 BC5228 CDS None chromosome 5132263 5133924 - L-lactate permease (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 387

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.