Organism : Bacillus cereus ATCC14579 | Module List:
Module 414 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 414

There are 13 regulatory influences for Module 414

Regulator Table (13)
Regulator Name Type
BC4001 tf
BC4211 tf
BC3194 tf
BC1490 tf
BC1715 tf
BC0648 tf
BC3690 tf
BC2988 tf
BC1059 tf
BC3438 tf
BC3704 tf
BC5363 tf
BC4570 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
4738 6.20e-02 aaAGGagg
Loader icon
4739 1.40e+04 GCcGacAatCcCCc
Loader icon
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 414 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 2.58e-02 4.15e-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 414

There are 33 genes in Module 414

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0509 BC0509 CDS None chromosome 494991 496727 + Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) False
BC0555 BC0555 CDS None chromosome 533657 535207 - Glycine betaine transporter (NCBI ptt file) False
BC1151 BC1151 CDS None chromosome 1130324 1130878 - IG hypothetical 17028 (NCBI ptt file) False
BC1443 BC1443 CDS None chromosome 1402824 1403600 - SAM-dependent methyltransferase (NCBI ptt file) False
BC1597 BC1597 CDS None chromosome 1558450 1558836 - Ribonuclease HI (NCBI ptt file) False
BC1614 BC1614 CDS None chromosome 1572144 1572974 + Multidrug-efflux transporter 2 regulator (NCBI ptt file) True
BC2055 BC2055 CDS None chromosome 1997737 1998954 - Macrolide-efflux protein (NCBI ptt file) False
BC2277 BC2277 CDS None chromosome 2218845 2219180 + hypothetical protein (NCBI ptt file) False
BC3000 BC3000 CDS None chromosome 2957421 2958878 - Proline/betaine transporter (NCBI ptt file) False
BC3194 BC3194 CDS None chromosome 3168963 3169382 - Transcriptional regulator, MarR family (NCBI ptt file) True
BC3311 BC3311 CDS None chromosome 3277663 3277911 - hypothetical protein (NCBI ptt file) False
BC3314 BC3314 CDS None chromosome 3279476 3280675 + Quinolone resistence NorA protein (NCBI ptt file) False
BC3343 BC3343 CDS None chromosome 3305636 3305884 - Integral membrane protein (NCBI ptt file) False
BC3344 BC3344 CDS None chromosome 3306088 3306555 + Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) False
BC3404 BC3404 CDS None chromosome 3367766 3368113 + Transcriptional regulator, MarR family (NCBI ptt file) True
BC3649 BC3649 DUMMY None chromosome 0 0 + None False
BC3704 BC3704 CDS None chromosome 3668166 3668825 + LexA repressor (NCBI ptt file) True
BC3711 BC3711 CDS None chromosome 3675704 3676669 + DNA integration/recombination/invertion protein (NCBI ptt file) False
BC3794 BC3794 CDS None chromosome 3769052 3769255 - hypothetical protein (NCBI ptt file) False
BC3795 BC3795 CDS None chromosome 3769252 3770001 - Translocation-enhancing protein tepA (NCBI ptt file) False
BC3935 BC3935 CDS None chromosome 3915660 3915908 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC4019 BC4019 CDS None chromosome 3996164 3996595 + hypothetical protein (NCBI ptt file) False
BC4088 BC4088 CDS None chromosome 4056994 4057740 - IG hypothetical 17224 (NCBI ptt file) False
BC4531 BC4531 CDS None chromosome 4477576 4478079 + hypothetical protein (NCBI ptt file) False
BC4726 BC4726 CDS None chromosome 4661402 4661725 - hypothetical protein (NCBI ptt file) False
BC4808 BC4808 CDS None chromosome 4732852 4733520 + Thiamine transporter (NCBI ptt file) False
BC4817 BC4817 CDS None chromosome 4740131 4740640 - hypothetical protein (NCBI ptt file) False
BC4819 BC4819 CDS None chromosome 4741527 4742474 + hypothetical protein (NCBI ptt file) False
BC4862 BC4862 CDS None chromosome 4785528 4786250 + Lipase (NCBI ptt file) False
BC4958 BC4958 CDS None chromosome 4870583 4871164 + NAD(P)H dehydrogenase [quinone] (NCBI ptt file) False
BC5379 BC5379 CDS None chromosome 5295520 5296824 - dGTP triphosphohydrolase (NCBI ptt file) False
BC5418 BC5418 CDS None chromosome 5333704 5334903 - Transporter, MFS superfamily (NCBI ptt file) False
BC5441 BC5441 CDS None chromosome 5363197 5364966 - Autolysin sensor kinase (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 414

Please add your comments for this module by using the form below. Your comments will be publicly available.

comments powered by Disqus
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.