Organism : Bacillus cereus ATCC14579 | Module List:
Module 85 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 85

There are 15 regulatory influences for Module 85

Regulator Table (15)
Regulator Name Type
BC3961 tf
BC2362 tf
BC0950 tf
BC3434 tf
BC0224 tf
BC4650 tf
BC0882 tf
BC2742 tf
BC5059 tf
BC2470 tf
BC2551 tf
BC3522 tf
BC2379 tf
BC3449 tf
BC3400 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
4088 1.60e+02 A.CaCCTctT
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4089 4.10e+04 GcCCATtTcaGCATcGaGG
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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 85 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Signal Transduction kegg subcategory 6.10e-03 1.71e-02 3/47
Two-component system kegg pathway 6.10e-03 1.71e-02 3/47

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 85

There are 47 genes in Module 85

Gene Member Table (47)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0222 BC0222 CDS None chromosome 199471 200418 + Periplasmic molybdate-binding protein (NCBI ptt file) False
BC0358 BC0358 CDS None chromosome 337629 337952 + Quaternary ammonium compound-resistance protein (NCBI ptt file) False
BC0399 BC0399 CDS None chromosome 378602 380128 - Oxidoreductase (NCBI ptt file) False
BC0494 BC0494 CDS None chromosome 485536 485655 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC0563 BC0563 CDS None chromosome 547077 547331 + Biotin carboxyl carrier protein (NCBI ptt file) False
BC0675 BC0675 CDS None chromosome 674475 674678 + hypothetical protein (NCBI ptt file) False
BC0771 BC0771 CDS None chromosome 758253 758534 + Protein erfK/srfK precursor (NCBI ptt file) False
BC0881 BC0881 CDS None chromosome 859008 861311 + Sensor protein comP (NCBI ptt file) False
BC0882 BC0882 CDS None chromosome 861347 862003 + Two-component response regulator comA (NCBI ptt file) True
BC0899 BC0899 CDS None chromosome 887981 888310 + hypothetical protein (NCBI ptt file) False
BC0923 BC0923 CDS None chromosome 909941 910051 + hypothetical protein (NCBI ptt file) False
BC0924 BC0924 CDS None chromosome 910554 910649 + hypothetical protein (NCBI ptt file) False
BC0929 BC0929 CDS None chromosome 912232 912624 + hypothetical protein (NCBI ptt file) False
BC0934 BC0934 CDS None chromosome 915196 915651 - hypothetical protein (NCBI ptt file) False
BC0944 BC0944 CDS None chromosome 928608 930191 + hypothetical protein (NCBI ptt file) False
BC0945 BC0945 CDS None chromosome 930675 931523 + DNA integration/recombination/invertion protein (NCBI ptt file) False
BC0950 BC0950 CDS None chromosome 940078 940242 + Transcriptional regulator, copG family (NCBI ptt file) True
BC0985 BC0985 CDS None chromosome 970010 970372 - hypothetical protein (NCBI ptt file) False
BC1073 BC1073 CDS None chromosome 1060096 1060395 + hypothetical protein (NCBI ptt file) False
BC1109 BC1109 CDS None chromosome 1089754 1090611 + hypothetical protein (NCBI ptt file) False
BC1623 BC1623 CDS None chromosome 1580699 1580887 + Hfq protein (NCBI ptt file) False
BC1656 BC1656 CDS None chromosome 1610101 1610901 - Flagellin (NCBI ptt file) False
BC1660 BC1660 CDS None chromosome 1614053 1614811 + Soluble lytic murein transglycosylase (NCBI ptt file) False
BC1848 BC1848 CDS None chromosome 1805567 1806664 + Prophage helix-turn-helix protein (NCBI ptt file) False
BC1935 BC1935 CDS None chromosome 1879520 1880059 + hypothetical protein (NCBI ptt file) False
BC2253 BC2253 CDS None chromosome 2202781 2202996 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC2362 BC2362 CDS None chromosome 2306995 2307861 - Transcriptional regulators, LysR family (NCBI ptt file) True
BC2379 BC2379 CDS None chromosome 2323045 2323602 + Transcriptional regulator (NCBI ptt file) True
BC2465 BC2465 CDS None chromosome 2430743 2430940 + hypothetical protein (NCBI ptt file) False
BC2470 BC2470 CDS None chromosome 2438668 2439498 + ECF-type sigma factor negative effector (NCBI ptt file) True
BC2474 BC2474 CDS None chromosome 2445073 2445633 + Ribosomal-protein-serine acetyltransferase (NCBI ptt file) False
BC2495 BC2495 CDS None chromosome 2463927 2464535 - hypothetical protein (NCBI ptt file) False
BC2552 BC2552 CDS None chromosome 2527072 2527335 + hypothetical protein (NCBI ptt file) False
BC2570 BC2570 CDS None chromosome 2540133 2540837 - Collagen triple helix repeat protein (NCBI ptt file) False
BC2622 BC2622 CDS None chromosome 2586027 2587028 + Macrolide glycosyltransferase (NCBI ptt file) False
BC2819 BC2819 CDS None chromosome 2784800 2785252 + hypothetical protein (NCBI ptt file) False
BC2961 BC2961 CDS None chromosome 2918870 2919886 - Sugar transport system permease protein (NCBI ptt file) False
BC3097 BC3097 CDS None chromosome 3053729 3054808 - Spore germination protein QC (NCBI ptt file) False
BC3138 BC3138 CDS None chromosome 3108604 3109173 + hypothetical protein (NCBI ptt file) False
BC3232 BC3232 CDS None chromosome 3214417 3214632 - hypothetical protein (NCBI ptt file) False
BC3238 BC3238 CDS None chromosome 3217032 3217445 - hypothetical protein (NCBI ptt file) False
BC3434 BC3434 CDS None chromosome 3395917 3396879 + Transcriptional regulator, DeoR family (NCBI ptt file) True
BC3689 BC3689 CDS None chromosome 3656256 3656912 - Site-specific recombinase (NCBI ptt file) False
BC3714 BC3714 CDS None chromosome 3679567 3680520 - tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI ptt file) False
BC3989 BC3989 CDS None chromosome 3963172 3964389 - Diguanylate cyclase/phosphodiesterase domain 2 (EAL) (NCBI ptt file) False
BC4945 BC4945 DUMMY None chromosome 0 0 + None False
BC5403 BC5403 CDS None chromosome 5317458 5318084 + Integral membrane protein (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 85

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.