Organism : Bacillus subtilis | Module List:
Module 66 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 66

There are 11 regulatory influences for Module 66

Regulator Table (11)
Regulator Name Type
BSU02680 tf
BSU33990 tf
BSU18420 tf
BSU13880 tf
BSU09510 tf
BSU05670 tf
BSU24770 tf
BSU08990 tf
BSU35050 tf
BSU34170 tf
BSU05330 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
5088 1.20e+03 GaAAGGaaTGA
Loader icon
5089 2.30e+02 AAaaaaaCaGCtT.C
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 66 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.87e-02 2.91e-02 14/30
Poorly characterized cog category 2.77e-02 4.21e-02 9/30
Lipid transport and metabolism cog subcategory 7.92e-03 1.29e-02 3/30
Arabinose efflux permease cog 8.00e-05 1.95e-04 3/30
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 66

There are 30 genes in Module 66

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU00570 yabM CDS None chromosome 64815 66413 + putative exporter (RefSeq) False
BSU00580 yabN CDS None chromosome 66403 67872 + putative fusion methylase and nucleotide pyrophosphohydrolase (RefSeq) False
BSU02270 pssA CDS None chromosome 247732 248265 + phosphatidylserine synthase (RefSeq) False
BSU05680 ydgK CDS None chromosome 613186 614394 + putative efflux transporter (RefSeq) False
BSU06330 yeaC CDS None chromosome 687535 688497 + hypothetical protein (RefSeq) False
BSU06340 yeaD CDS None chromosome 688881 689693 + hypothetical protein (RefSeq) False
BSU06380 yebC CDS None chromosome 695535 696338 + putative integral inner membrane protein (RefSeq) False
BSU07500 yfmE CDS None chromosome 823053 824054 - iron-dicitrate ABC transporter (permease) (RefSeq) False
BSU07980 pdaA CDS None chromosome 868894 869685 + exported N-acetylmuramic acid deacetylase (RefSeq) False
BSU09000 yhbJ CDS None chromosome 976406 977071 + putative integral inner membrane protein; putative exporter subunit (RefSeq) False
BSU09020 yhcB CDS None chromosome 978733 979263 + putative oxidoreductase associated to oxygen stress (RefSeq) False
BSU13090 ykkC CDS None chromosome 1375823 1376161 + efflux transporter (RefSeq) False
BSU13100 ykkD CDS None chromosome 1376161 1376478 + efflux transporter (RefSeq) False
BSU13880 glcT CDS None chromosome 1455400 1456257 + transcriptional antiterminator (BglG family) (RefSeq) True
BSU16825 BSU16825 DUMMY None chromosome 0 0 + None False
BSU19230 yocJ CDS None chromosome 2095561 2096187 - azoreductase (RefSeq) False
BSU19530 yodA CDS None chromosome 2125748 2126137 + putative tautomerase (RefSeq) False
BSU20040 nrdF CDS None chromosome 2159179 2160976 - ribonucleotide-diphosphate reductase subunit beta (NCBI) False
BSU21730 ypmS CDS None chromosome 2289481 2290044 - hypothetical protein (RefSeq) False
BSU22160 yptA CDS None chromosome 2328712 2328903 - hypothetical protein (RefSeq) False
BSU23600 yqxK CDS None chromosome 2456537 2457421 - hypothetical protein (RefSeq) False
BSU23800 proI CDS None chromosome 2472340 2473176 + pyrroline-5-carboxylate reductase (RefSeq) False
BSU27090 aapA CDS None chromosome 2765783 2767162 + d-Serine/d-alanine/glycine permease (RefSeq) False
BSU27210 yrhF CDS None chromosome 2779752 2780120 - hypothetical protein (RefSeq) False
BSU29970 ytkP CDS None chromosome 3065500 3066435 + putative cysteine synthase-like protein (RefSeq) False
BSU31130 yubD CDS None chromosome 3190882 3192417 - putative efflux transporter (RefSeq) False
BSU33100 liaF CDS None chromosome 3395141 3395866 - integral inner membrane protein (RefSeq) False
BSU33990 yvbU CDS None chromosome 3487005 3487883 - putative transcriptional regulator (LysR family) (RefSeq) True
BSU36590 clsA CDS None chromosome 3761686 3763134 + cardiolipin synthase (RefSeq) False
BSU36990 ywkF CDS None chromosome 3794893 3795180 - hypothetical protein (RefSeq) 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.