Organism : Bacillus subtilis | Module List:
Module 339 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 339

There are 10 regulatory influences for Module 339

Regulator Table (10)
Regulator Name Type
BSU03080 tf
BSU26720 tf
BSU33740 tf
BSU30460 tf
BSU08300 tf
BSU30020 tf
BSU26390 tf
BSU40670 tf
BSU28400 tf
BSU04060 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
5612 1.00e+00 AGCaTGTTcTc.TtTTgttGct
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5613 4.10e+01 AaATaAAacAtgagCCTTtTGgcA
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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 339 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.80e-02 2.82e-02 8/30
Transcription cog subcategory 3.35e-03 5.68e-03 6/30
Defense mechanisms cog subcategory 3.20e-05 9.40e-05 4/30
Signal transduction mechanisms cog subcategory 2.61e-02 3.98e-02 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 339

There are 30 genes in Module 339

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU03070 mdr CDS None chromosome 332258 333538 - multidrug-efflux transporter (RefSeq) False
BSU03080 ycgE CDS None chromosome 333651 334118 + putative transcriptional regulator (RefSeq) True
BSU08350 estB CDS None chromosome 909354 909986 + secreted esterase / lipase (RefSeq) False
BSU09050 yhcE CDS None chromosome 979810 980571 + putative integral inner membrane orphan protein (RefSeq) False
BSU09070 yhcG CDS None chromosome 980941 981639 + putative ABC transporter ATP-binding protein (RefSeq) False
BSU12240 yjkA CDS None chromosome 1294306 1295058 - putative ABC transporter (permease) (RefSeq) False
BSU12250 yjkB CDS None chromosome 1295058 1295810 - putative phosphate ABC transporter (ATP-binding protein) (RefSeq) False
BSU17790 yndH CDS None chromosome 1911548 1912165 + hypothetical protein (RefSeq) False
BSU17810 yndK CDS None chromosome 1913839 1914204 + putative phage/plasmid replication protein (RefSeq) False
BSU26700 azlD CDS None chromosome 2727873 2728205 - branched-chain amino acid transporter (RefSeq) False
BSU26710 azlC CDS None chromosome 2728202 2728966 - branched-chain amino acid transporter (RefSeq) False
BSU26720 azlB CDS None chromosome 2728979 2729452 - transcriptional regulator (Lrp/AsnC family) (RefSeq) True
BSU28650 ysgA CDS None chromosome 2929895 2930641 - putative RNA methylase (RefSeq) False
BSU28920 lytT CDS None chromosome 2954824 2955549 - two-component response regulator [LytS] (RefSeq) False
BSU28930 lytS CDS None chromosome 2955527 2957308 - two-component sensor histidine kinase [LytT] (RefSeq) False
BSU28940 ysaA CDS None chromosome 2957475 2958257 + putative phosphatase (RefSeq) False
BSU30430 ytrD CDS None chromosome 3115038 3116015 - ABC transporter, permease component (RefSeq) False
BSU30440 ytrC CDS None chromosome 3116045 3117031 - ABC transporter, permease component (RefSeq) False
BSU30450 ytrB CDS None chromosome 3117025 3117903 - ABC transporter (ATP-binding protein) (RefSeq) False
BSU30460 ytrA CDS None chromosome 3117896 3118288 - transcriptional regulator (GntR family) (RefSeq) True
BSU30810 ytxM CDS None chromosome 3148799 3149623 - putative esterase (RefSeq) False
BSU33330 lysP CDS None chromosome 3418686 3420095 - lysine permease (RefSeq) False
BSU33460 yvgT CDS None chromosome 3435879 3436487 - putative integral inner membrane protein (RefSeq) False
BSU33740 yvaV CDS None chromosome 3462556 3463098 + putative transcriptional regulator (RefSeq) True
BSU34700 yvcR CDS None chromosome 3564526 3565305 - putative ABC transporter (ATP-binding protein) (RefSeq) False
BSU34720 yvcP CDS None chromosome 3566452 3567165 - two-component response regulator [YvcQ] (RefSeq) False
BSU34820 bmrA CDS None chromosome 3576775 3578544 - efflux transporter (ATP-binding and permease protein) (RefSeq) False
BSU36220 ywqG CDS None chromosome 3727538 3728323 - hypothetical protein (RefSeq) False
BSU36240 ywqE CDS None chromosome 3730032 3730796 - protein tyrosine-phosphatase (RefSeq) False
BSU40490 yycA CDS None chromosome 4160127 4162184 + putative integral inner membrane protein; putative glycosyl transferase (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.

Comments for Module 339

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.