Organism : Bacillus cereus ATCC14579 | Module List:
Module 517 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 517

There are 11 regulatory influences for Module 517

Regulator Table (11)
Regulator Name Type
BC1531 tf
BC1715 tf
BC4703 tf
BC0954 tf
BC3332 tf
BC0059 tf
BC1841 tf
BC0975 tf
BC5175 tf
BC2218 tf
BC0649 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
4944 9.10e+01 atGtgAAAgggGGgc
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4945 1.10e+03 taaAagggGtG
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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 517 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes tigr mainrole 8.54e-03 1.10e-02 3/33
Sporulation and germination tigr sub1role 2.42e-03 3.58e-03 3/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Function unknown cog subcategory 2.71e-02 4.34e-02 5/33
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 517

There are 33 genes in Module 517

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0059 BC0059 CDS None chromosome 57952 58488 + Stage V sporulation protein T (NCBI ptt file) True
BC0559 BC0559 CDS None chromosome 541041 543017 + Methyl-accepting chemotaxis protein (NCBI ptt file) False
BC0692 BC0692 CDS None chromosome 691852 692289 - Acetyltransferase (NCBI ptt file) False
BC0844 BC0844 CDS None chromosome 823095 823499 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC1072 BC1072 CDS None chromosome 1057746 1059962 + Endonuclease/Exonuclease/phosphatase family protein (NCBI ptt file) False
BC1139 BC1139 CDS None chromosome 1124229 1124516 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC1263 BC1263 CDS None chromosome 1239584 1239691 + Phage integrase family protein (NCBI ptt file) False
BC1359 BC1359 CDS None chromosome 1330429 1331331 + Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) False
BC1628 BC1628 CDS None chromosome 1583869 1585887 + Chemotaxis protein cheA (NCBI ptt file) False
BC1715 BC1715 CDS None chromosome 1663034 1663798 + Transcriptional regulator (NCBI ptt file) True
BC1716 BC1716 CDS None chromosome 1663896 1665305 + Na+ driven multidrug efflux pump (NCBI ptt file) False
BC1761 BC1761 CDS None chromosome 1713726 1714985 + GTP-binding protein hflX (NCBI ptt file) False
BC1996 BC1996 CDS None chromosome 1944678 1944965 + Transcription state regulatory protein abrB (NCBI ptt file) True
BC2095 BC2095 CDS None chromosome 2039794 2040222 + hypothetical protein (NCBI ptt file) False
BC2160 BC2160 CDS None chromosome 2103260 2103589 + hypothetical protein (NCBI ptt file) False
BC2212 BC2212 CDS None chromosome 2157205 2157399 + hypothetical protein (NCBI ptt file) False
BC2218 BC2218 CDS None chromosome 2162168 2163022 + Transcriptional regulator, RpiR family (NCBI ptt file) True
BC2221 BC2221 CDS None chromosome 2165532 2166581 - Oligopeptide transport system permease protein oppC (NCBI ptt file) False
BC2375 BC2375 CDS None chromosome 2320199 2320483 - hypothetical protein (NCBI ptt file) False
BC2392 BC2392 CDS None chromosome 2336100 2337659 - FenI (NCBI ptt file) False
BC2464 BC2464 CDS None chromosome 2428176 2429627 + S-layer protein / Peptidoglycan endo-beta-N-acetylglucosaminidase (NCBI ptt file) False
BC2666 BC2666 CDS None chromosome 2650815 2651321 + hypothetical protein (NCBI ptt file) False
BC2726 BC2726 CDS None chromosome 2702565 2702714 - hypothetical protein (NCBI ptt file) False
BC2727 BC2727 CDS None chromosome 2702707 2703015 - hypothetical protein (NCBI ptt file) False
BC3055 BC3055 CDS None chromosome 3012786 3013766 - hypothetical protein (NCBI ptt file) False
BC3088 BC3088 CDS None chromosome 3045340 3046197 + Metal-dependent hydrolase (NCBI ptt file) False
BC3331 BC3331 CDS None chromosome 3295014 3295373 + hypothetical protein (NCBI ptt file) False
BC3536 BC3536 CDS None chromosome 3504399 3504746 - hypothetical protein (NCBI ptt file) False
BC3618 BC3618 CDS None chromosome 3593201 3593842 - Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) False
BC4232 BC4232 CDS None chromosome 4182015 4182485 - Shikimate kinase (NCBI ptt file) False
BC4385 BC4385 CDS None chromosome 4324144 4325211 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC4466 BC4466 CDS None chromosome 4412445 4413470 - CotS-related protein (NCBI ptt file) False
BC5490 BC5490 CDS None chromosome 5411393 5411527 - LSU ribosomal protein L34P (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 517

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.