Organism : Bacillus cereus ATCC14579 | Module List:
Module 188 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 188

There are 15 regulatory influences for Module 188

Regulator Table (15)
Regulator Name Type
BC5141 tf
BC0158 tf
BC0122 tf
BC0042 tf
BC1387 tf
BC3706 tf
BC4842 tf
BC1841 tf
BC1075 tf
BC0806 tf
BC3128 tf
BC4708 tf
BC0265 tf
BC3253 tf
BC3976 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
4292 2.00e+00 gCcaa.gAAAGcG
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4293 2.60e+02 ggaCatacagacAtg
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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 188 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 1.30e-05 12/19
Carbohydrate Metabolism kegg subcategory 0.00e+00 1.00e-06 8/19
Glycolysis / Gluconeogenesis kegg pathway 0.00e+00 0.00e+00 7/19
Citrate cycle (TCA cycle) kegg pathway 0.00e+00 1.00e-06 4/19
Pyruvate metabolism kegg pathway 1.00e-06 2.60e-05 4/19
Energy Metabolism kegg subcategory 0.00e+00 1.50e-05 6/19
Oxidative phosphorylation kegg pathway 1.00e-06 2.20e-05 4/19
Amino Acid Metabolism kegg subcategory 1.70e-02 3.53e-02 3/19
Global kegg category 1.00e-06 2.20e-05 11/19
Metabolism kegg subcategory 1.00e-06 2.20e-05 11/19
Metabolic pathways kegg pathway 0.00e+00 8.00e-06 11/19
Biosynthesis of secondary metabolites kegg pathway 5.00e-06 1.19e-04 7/19
Microbial metabolism in diverse environments kegg pathway 0.00e+00 1.20e-05 7/19

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 0.00e+00 0.00e+00 8/19
Electron transport tigr sub1role 0.00e+00 0.00e+00 4/19
Glycolysis/gluconeogenesis tigr sub1role 0.00e+00 1.00e-06 3/19

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.00e-06 6.00e-06 14/19
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 8/19
Carbohydrate transport and metabolism cog subcategory 7.00e-06 3.10e-05 6/19
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 188

There are 19 genes in Module 188

Gene Member Table (19)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0128 BC0128 CDS None chromosome 122698 124776 + Protein Translation Elongation Factor G (EF-G) (NCBI ptt file) False
BC0129 BC0129 CDS None chromosome 124894 126081 + Protein Translation Elongation Factor Tu (EF-TU) (NCBI ptt file) False
BC0695 BC0695 CDS None chromosome 694661 694972 - Cytochrome aa3 quinol oxidase polypeptide IV (NCBI ptt file) False
BC0696 BC0696 CDS None chromosome 694973 695575 - Cytochrome aa3 quinol oxidase polypeptide III (NCBI ptt file) False
BC0697 BC0697 CDS None chromosome 695589 697532 - Cytochrome aa3 quinol oxidase polypeptide I (NCBI ptt file) False
BC0698 BC0698 CDS None chromosome 697557 698432 - Cytochrome aa3 quinol oxidase polypeptide II (NCBI ptt file) False
BC3970 BC3970 CDS None chromosome 3945300 3946712 - Dihydrolipoamide dehydrogenase (NCBI ptt file) False
BC3971 BC3971 CDS None chromosome 3946718 3948007 - Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (NCBI ptt file) False
BC3972 BC3972 CDS None chromosome 3948101 3949078 - Pyruvate dehydrogenase E1 component beta subunit (NCBI ptt file) False
BC3973 BC3973 CDS None chromosome 3949082 3950197 - Pyruvate dehydrogenase E1 component alpha subunit (NCBI ptt file) False
BC4048 BC4048 CDS None chromosome 4019780 4021492 - Phosphoenolpyruvate-protein phosphotransferase (NCBI ptt file) False
BC4049 BC4049 CDS None chromosome 4021492 4021755 - Phosphocarrier protein HPr (NCBI ptt file) False
BC4050 BC4050 CDS None chromosome 4021891 4023954 - PTS system, glucose-specific IIABC component (NCBI ptt file) False
BC5135 BC5135 CDS None chromosome 5037710 5039005 - Enolase (NCBI ptt file) False
BC5136 BC5136 CDS None chromosome 5039036 5040565 - Phosphoglycerate mutase (NCBI ptt file) False
BC5137 BC5137 DUMMY None chromosome 0 0 + None False
BC5140 BC5140 CDS None chromosome 5042675 5043661 - Glyceraldehyde 3-phosphate dehydrogenase (NCBI ptt file) False
BC5141 BC5141 CDS None chromosome 5043707 5044750 - Central glycolytic genes regulator (NCBI ptt file) True
VIMSS12791523 VIMSS12791523 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 188

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.