Organism : Bacillus cereus ATCC14579 | Module List:
Module 252 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 252

There are 13 regulatory influences for Module 252

Regulator Table (13)
Regulator Name Type
BC3813 tf
BC1731 tf
BC3332 tf
BC3062 tf
BC5340 tf
BC4316 tf
BC3653 tf
BC3814 tf
BC2631 tf
BC0059 tf
BC1850 tf
BC2133 tf
BC1531 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
4420 7.90e+01 ataaaaAAaGagGatgaAAtAc
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4421 9.60e+03 GCCCcC
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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 252 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Genetic Information Processing kegg category 3.97e-04 3.24e-03 5/25
Replication and Repair kegg subcategory 3.00e-06 7.80e-05 4/25
Environmental Information Processing kegg category 9.57e-03 2.32e-02 4/25
Signal Transduction kegg subcategory 5.63e-04 4.03e-03 3/25
Two-component system kegg pathway 5.63e-04 4.03e-03 3/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA metabolism tigr mainrole 2.93e-04 5.52e-04 3/25
DNA replication, recombination, and repair tigr sub1role 1.95e-04 3.83e-04 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 2.30e-03 4.31e-03 8/25
Cellular processes and signaling cog category 1.34e-03 2.61e-03 8/25
Replication, recombination and repair cog subcategory 2.00e-06 1.20e-05 6/25
Signal transduction mechanisms cog subcategory 1.60e-04 3.85e-04 5/25
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 252

There are 25 genes in Module 252

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0024 BC0024 CDS None chromosome 25392 27080 + DNA polymerase III subunit gamma/tau (NCBI ptt file) False
BC0286 BC0286 CDS None chromosome 250304 250777 + ATP/GTP hydrolase (NCBI ptt file) False
BC0341 BC0341 CDS None chromosome 317208 319217 + NAD-dependent DNA ligase (NCBI ptt file) False
BC0468 BC0468 CDS None chromosome 458158 459021 + DNA-3-methyladenine glycosylase II (NCBI ptt file) False
BC0497 BC0497 CDS None chromosome 487835 488740 - Cell division inhibitor (NCBI ptt file) False
BC0609 BC0609 CDS None chromosome 600194 600580 + Lactoylglutathione lyase (NCBI ptt file) False
BC0694 BC0694 CDS None chromosome 692614 694461 - Na+/H+ antiporter NapA (NCBI ptt file) False
BC1035 BC1035 CDS None chromosome 1015849 1017339 + Glycerol kinase (NCBI ptt file) False
BC1300 BC1300 CDS None chromosome 1279542 1280213 + Two-component response regulator (NCBI ptt file) False
BC1301 BC1301 CDS None chromosome 1280217 1281617 + Two component system histidine kinase (NCBI ptt file) False
BC1742 BC1742 CDS None chromosome 1689173 1690462 + Two component system histidine kinase (NCBI ptt file) False
BC1743 BC1743 CDS None chromosome 1690465 1691397 + Two-component response regulator (NCBI ptt file) False
BC1804 BC1804 CDS None chromosome 1758444 1759403 + Rhodanese-related sulfurtransferases (NCBI ptt file) False
BC3843 BC3843 CDS None chromosome 3819462 3820811 - Signal recognition particle, subunit Ffh/SRP54 (NCBI ptt file) False
BC4295 BC4295 CDS None chromosome 4239077 4239823 - DNA repair protein recO (NCBI ptt file) False
BC4315 BC4315 CDS None chromosome 4257726 4258865 - Coproporphyrinogen oxidase, anaerobic (NCBI ptt file) False
BC4440 BC4440 CDS None chromosome 4380641 4381501 - Stage IV sporulation protein FB (NCBI ptt file) False
BC4579 BC4579 CDS None chromosome 4523907 4524845 - Primosomal protein dnaI (NCBI ptt file) False
BC4580 BC4580 CDS None chromosome 4524879 4526288 - Replication initiation and membrane attachment protein (NCBI ptt file) False
BC4673 BC4673 CDS None chromosome 4612757 4612933 - hypothetical protein (NCBI ptt file) False
BC5182 BC5182 CDS None chromosome 5078394 5080109 - Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) False
BC5457 BC5457 CDS None chromosome 5383834 5384019 - hypothetical protein (NCBI ptt file) False
BC5460 BC5460 CDS None chromosome 5386091 5386933 - hypothetical protein (NCBI ptt file) False
BC5462 BC5462 CDS None chromosome 5388227 5390068 - Two-component sensor kinase yycG (NCBI ptt file) False
BC5485 BC5485 CDS None chromosome 5405987 5407876 - Glucose inhibited division protein A (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 252

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.