Organism : Bacillus cereus ATCC14579 | Module List:
Module 217 Profile

GeneModule member RegulatorRegulator MotifMotif
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 217

There are 15 regulatory influences for Module 217

Regulator Table (15)
Regulator Name Type
BC3593 tf
BC1449 tf
BC0047 tf
BC0648 tf
BC5222 tf
BC5010 tf
BC0230 tf
BC0856 tf
BC3903 tf
BC4256 tf
BC1884 tf
BC4336 tf
BC5250 tf
BC3720 tf
BC1703 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
4350 6.20e-07 aagaaagGaGa
Loader icon
4351 9.40e+02 CCcTCC
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 217 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 1.28e-02 1.58e-02 3/37
Sporulation and germination tigr sub1role 3.70e-03 5.21e-03 3/37

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Defense mechanisms cog subcategory 2.33e-03 4.36e-03 3/37
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 217

There are 37 genes in Module 217

Gene Member Table (37)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0034 BC0034 CDS None chromosome 34129 34308 + CsfB protein (NCBI ptt file) False
BC0047 BC0047 CDS None chromosome 46055 46918 + Sporulation-specific protease YabG (NCBI ptt file) True
BC0288 BC0288 CDS None chromosome 251485 251907 + Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) False
BC0480 BC0480 CDS None chromosome 469359 469700 - hypothetical protein (NCBI ptt file) False
BC0818 BC0818 CDS None chromosome 802658 803497 + Oligopeptide transport system permease protein oppB (NCBI ptt file) False
BC0819 BC0819 CDS None chromosome 803499 804503 + Oligopeptide transport system permease protein oppC (NCBI ptt file) False
BC0870 BC0870 CDS None chromosome 846887 848647 + Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) False
BC0871 BC0871 CDS None chromosome 849019 850644 + Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) False
BC1141 BC1141 CDS None chromosome 1124908 1125282 - Spore germination protein PE (NCBI ptt file) False
BC1152 BC1152 CDS None chromosome 1131118 1132125 + Asparagine synthetase (NCBI ptt file) False
BC1243 BC1243 CDS None chromosome 1218016 1218786 + hypothetical protein (NCBI ptt file) False
BC1331 BC1331 CDS None chromosome 1306926 1309208 + Internalin (NCBI ptt file) False
BC1449 BC1449 CDS None chromosome 1408136 1408648 - cAMP-dependent protein kinase regulatory chain (NCBI ptt file) True
BC1568 BC1568 CDS None chromosome 1514376 1515122 + Methionine aminopeptidase (NCBI ptt file) False
BC1830 BC1830 CDS None chromosome 1786731 1788371 + Copper resistance protein A (NCBI ptt file) False
BC2378 BC2378 CDS None chromosome 2322348 2322932 - Transporter, LysE family (NCBI ptt file) False
BC2404 BC2404 CDS None chromosome 2348355 2348489 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC2417 BC2417 CDS None chromosome 2359786 2360250 - hypothetical protein (NCBI ptt file) False
BC2430 BC2430 CDS None chromosome 2373846 2374556 + Methyltransferase (NCBI ptt file) False
BC2465 BC2465 CDS None chromosome 2430743 2430940 + hypothetical protein (NCBI ptt file) False
BC2544 BC2544 CDS None chromosome 2517503 2519437 + ABC transporter permease protein (NCBI ptt file) False
BC2545 BC2545 CDS None chromosome 2519504 2520178 + hypothetical protein (NCBI ptt file) False
BC2711 BC2711 CDS None chromosome 2690002 2690781 - Bacitracin resistance protein (Putative undecaprenol kinase) (NCBI ptt file) False
BC2741 BC2741 CDS None chromosome 2720727 2721644 - Transporter, Drug/Metabolite Exporter family (NCBI ptt file) False
BC2744 BC2744 CDS None chromosome 2724618 2724953 - hypothetical protein (NCBI ptt file) False
BC3280 BC3280 CDS None chromosome 3256520 3256876 - hypothetical protein (NCBI ptt file) False
BC3474 BC3474 CDS None chromosome 3428154 3428630 - hypothetical protein (NCBI ptt file) False
BC3475 BC3475 CDS None chromosome 3428648 3429160 - hypothetical protein (NCBI ptt file) False
BC3593 BC3593 CDS None chromosome 3569404 3570372 - Transcriptional regulator, DeoR family (NCBI ptt file) True
BC3667 BC3667 CDS None chromosome 3635125 3635700 - ABC transporter permease protein (NCBI ptt file) False
BC3967 BC3967 CDS None chromosome 3944019 3944363 - hypothetical protein (NCBI ptt file) False
BC4304 BC4304 CDS None chromosome 4247054 4247347 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC4520 uvrC CDS None chromosome 4464276 4466060 - excinuclease ABC subunit C (RefSeq) False
BC4607 BC4607 CDS None chromosome 4555901 4556425 + hypothetical protein (NCBI ptt file) False
BC4641 BC4641 CDS None chromosome 4581443 4582081 - hypothetical protein (NCBI ptt file) False
BC4847 BC4847 CDS None chromosome 4770594 4771454 - D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) False
BC4858 BC4858 CDS None chromosome 4782674 4783405 + DnaK suppressor 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.

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.