Organism : Bacillus cereus ATCC14579 | Module List:
Module 337 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 337

There are 11 regulatory influences for Module 337

Regulator Table (11)
Regulator Name Type
BC4124 tf
BC5409 tf
BC5173 tf
BC5265 tf
BC5256 tf
BC1680 tf
BC3497 tf
BC0266 tf
BC4174 tf
BC5171 tf
BC3389 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
4586 2.30e-08 AaaAGGgG
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4587 9.30e+04 GggGGAC
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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 337 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Histidine metabolism kegg pathway 2.00e-05 3.63e-04 3/33

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 7.05e-03 9.25e-03 3/33
Amino acids and amines tigr sub1role 1.70e-05 4.60e-05 3/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Replication, recombination and repair cog subcategory 1.05e-02 1.80e-02 3/33
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 337

There are 33 genes in Module 337

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0335 BC0335 CDS None chromosome 312282 312446 - hypothetical protein (NCBI ptt file) False
BC0336 BC0336 CDS None chromosome 312462 313307 - Somatin-like protein (NCBI ptt file) False
BC1150 BC1150 CDS None chromosome 1129828 1130193 + IG hypothetical 15940 (NCBI ptt file) False
BC1432 BC1432 CDS None chromosome 1392819 1394093 + Proton/sodium-glutamate symport protein (NCBI ptt file) False
BC1680 BC1680 CDS None chromosome 1628637 1629851 - Transcriptional regulator, XRE family (NCBI ptt file) True
BC1755 BC1755 CDS None chromosome 1705372 1706175 + UDP-galactose-lipid carrier transferase (NCBI ptt file) False
BC2665 BC2665 CDS None chromosome 2649786 2650412 + Teicoplanin resistance protein vanZ (NCBI ptt file) False
BC2717 BC2717 CDS None chromosome 2694554 2694811 + hypothetical protein (NCBI ptt file) False
BC2718 BC2718 CDS None chromosome 2694903 2695082 + hypothetical protein (NCBI ptt file) False
BC2817 BC2817 CDS None chromosome 2783342 2784130 + hypothetical protein (NCBI ptt file) False
BC2841 BC2841 CDS None chromosome 2805361 2805669 - hypothetical protein (NCBI ptt file) False
BC2842 BC2842 CDS None chromosome 2805657 2806106 - hypothetical protein (NCBI ptt file) False
BC3061 BC3061 CDS None chromosome 3017461 3019614 - Penicillin-binding protein (NCBI ptt file) False
BC3437 BC3437 CDS None chromosome 3398725 3399066 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC3508 BC3508 CDS None chromosome 3462229 3462450 - hypothetical protein (NCBI ptt file) False
BC3648 BC3648 CDS None chromosome 3618998 3619474 - CarD-like transcriptional regulator (NCBI ptt file) True
BC3650 BC3650 CDS None chromosome 3620671 3621942 - Imidazolonepropionase (NCBI ptt file) False
BC3651 BC3651 CDS None chromosome 3621955 3623613 - Urocanate hydratase (NCBI ptt file) False
BC3652 BC3652 CDS None chromosome 3623637 3625157 - Histidine ammonia-lyase (NCBI ptt file) False
BC3740 BC3740 CDS None chromosome 3704462 3705058 + ADA regulatory protein (NCBI ptt file) True
BC3741 BC3741 CDS None chromosome 3705039 3705569 + O6-methylguanine-DNA methyltransferase (NCBI ptt file) False
BC3742 BC3742 CDS None chromosome 3705566 3706477 + DNA-3-methyladenine glycosylase II (NCBI ptt file) False
BC4124 BC4124 CDS None chromosome 4089179 4089625 + Transcriptional regulator, MarR family (NCBI ptt file) True
BC4152 BC4152 CDS None chromosome 4116380 4116865 - hypothetical protein (NCBI ptt file) False
BC4153 BC4153 CDS None chromosome 4116924 4117388 - Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) False
BC4245 BC4245 CDS None chromosome 4191184 4191495 + hypothetical protein (NCBI ptt file) False
BC4454 BC4454 CDS None chromosome 4395990 4396610 - hypothetical protein (NCBI ptt file) False
BC4953 BC4953 CDS None chromosome 4867567 4867782 + hypothetical protein (NCBI ptt file) False
BC5048 BC5048 CDS None chromosome 4951387 4951893 + Ferritin (NCBI ptt file) False
BC5170 BC5170 CDS None chromosome 5069156 5069776 - Integral membrane protein (NCBI ptt file) False
BC5171 BC5171 CDS None chromosome 5069773 5070537 - Transcriptional regulator, MerR family (NCBI ptt file) True
BC5172 BC5172 CDS None chromosome 5070635 5070862 - hypothetical protein (NCBI ptt file) False
BC5304 BC5304 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 337

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.