Organism : Bacillus cereus ATCC14579 | Module List:
Module 512 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 512

There are 19 regulatory influences for Module 512

Regulator Table (19)
Regulator Name Type
BC3155 tf
BC1814 tf
BC0851 tf
BC0975 tf
BC4589 tf
BC2353 tf
BC5265 tf
BC1134 tf
BC1915 tf
BC3405 tf
BC4081 tf
BC2217 tf
BC4206 tf
BC2760 tf
BC3033 tf
BC5409 tf
BC4499 tf
BC3175 tf
BC2631 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
4934 1.20e-03 GGGGGa
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4935 7.20e+03 CtGcaGGGC
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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 512 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 9.50e-05 1.13e-03 11/24
Amino Acid Metabolism kegg subcategory 2.30e-05 4.01e-04 7/24
Arginine and proline metabolism kegg pathway 0.00e+00 0.00e+00 7/24
Metabolism of Cofactors and Vitamins kegg subcategory 2.29e-04 2.18e-03 4/24
Riboflavin metabolism kegg pathway 0.00e+00 0.00e+00 4/24
Environmental Information Processing kegg category 8.00e-03 2.06e-02 4/24
Signal Transduction kegg subcategory 2.90e-05 4.76e-04 4/24
Two-component system kegg pathway 2.90e-05 4.76e-04 4/24
Global kegg category 3.00e-06 7.10e-05 12/24
Metabolism kegg subcategory 3.00e-06 7.10e-05 12/24
Metabolic pathways kegg pathway 6.00e-06 1.39e-04 11/24
Biosynthesis of secondary metabolites kegg pathway 4.00e-06 9.90e-05 8/24

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 1.63e-03 2.53e-03 3/24
Amino acid biosynthesis tigr mainrole 1.00e-06 2.00e-06 5/24
Glutamate family tigr sub1role 0.00e+00 0.00e+00 5/24
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 8.31e-04 1.39e-03 3/24
Riboflavin, FMN, and FAD tigr sub1role 0.00e+00 0.00e+00 3/24

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 19/24
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 11/24
Coenzyme transport and metabolism cog subcategory 4.37e-04 9.32e-04 4/24
Inorganic ion transport and metabolism cog subcategory 1.55e-02 2.59e-02 3/24
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 512

There are 24 genes in Module 512

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0403 BC0403 CDS None chromosome 383565 384287 - Glutamine transport ATP-binding protein glnQ (NCBI ptt file) False
BC0666 BC0666 CDS None chromosome 662377 664776 + Immune inhibitor A precursor (NCBI ptt file) False
BC0753 BC0753 CDS None chromosome 738869 740536 + Potassium-transporting ATPase A chain (NCBI ptt file) False
BC0754 BC0754 CDS None chromosome 740547 742640 + Potassium-transporting ATPase B chain (NCBI ptt file) False
BC0755 BC0755 CDS None chromosome 742657 743238 + Potassium-transporting ATPase C chain (NCBI ptt file) False
BC0756 BC0756 CDS None chromosome 743304 744449 + Sensor protein kdpD (NCBI ptt file) False
BC0849 BC0849 CDS None chromosome 826317 826772 + Amino acid acetyltransferase (NCBI ptt file) False
BC3031 BC3031 CDS None chromosome 2992004 2993029 - Isoflavone reductase (NCBI ptt file) False
BC3346 BC3346 CDS None chromosome 3309586 3312060 - Collagen-like triple helix repeat protein (NCBI ptt file) False
BC4109 BC4109 CDS None chromosome 4073304 4074443 + Diaminohydroxyphosphoribosylaminopyrimidine deaminase (NCBI ptt file) False
BC4110 BC4110 CDS None chromosome 4074425 4075069 + Riboflavin synthase alpha chain (NCBI ptt file) False
BC4111 BC4111 CDS None chromosome 4075082 4076275 + GTP cyclohydrolase II (NCBI ptt file) False
BC4112 BC4112 CDS None chromosome 4076294 4076755 + 6,7-dimethyl-8-ribityllumazine synthase (NCBI ptt file) False
BC4126 BC4126 CDS None chromosome 4090622 4091572 - Ornithine carbamoyltransferase (NCBI ptt file) False
BC4127 argD CDS None chromosome 4091585 4092745 - acetylornithine aminotransferase (RefSeq) False
BC4128 BC4128 CDS None chromosome 4092742 4093509 - Acetylglutamate kinase (NCBI ptt file) False
BC4129 BC4129 CDS None chromosome 4093521 4094747 - Glutamate N-acetyltransferase (NCBI ptt file) False
BC4130 BC4130 DUMMY None chromosome 0 0 + None False
BC4148 BC4148 CDS None chromosome 4113393 4114115 - Arginine transport ATP-binding protein artP (NCBI ptt file) False
BC4149 BC4149 CDS None chromosome 4114108 4114767 - Arginine transport system permease protein artQ (NCBI ptt file) False
BC4150 BC4150 CDS None chromosome 4114804 4115583 - Arginine-binding protein (NCBI ptt file) False
BC4628 BC4628 CDS None chromosome 4570289 4570627 - hypothetical protein (NCBI ptt file) False
BC4629 BC4629 CDS None chromosome 4570741 4572129 - Argininosuccinate lyase (NCBI ptt file) False
BC4630 BC4630 CDS None chromosome 4572126 4573331 - Argininosuccinate synthase (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 512

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.