Organism : Bacillus subtilis | Module List:
Module 306 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 306

There are 13 regulatory influences for Module 306

Regulator Table (13)
Regulator Name Type
BSU40050 tf
BSU30150 tf
BSU27080 tf
BSU11930 tf
BSU40710 tf
BSU40410 tf
BSU26870 tf
BSU37290 tf
BSU27320 tf
BSU34380 tf
BSU00370 tf
BSU36420 tf
BSU26220 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
5550 2.00e-01 ccCTCCttTac
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5551 2.30e+04 GCCGTC
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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 306 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
NRPS-para261 tigrfam 0.00e+00 0.00e+00 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.69e-03 2.98e-03 15/27
Lipid transport and metabolism cog subcategory 6.20e-05 1.54e-04 5/27
Secondary metabolites biosynthesis, transport and catabolism cog subcategory 0.00e+00 0.00e+00 10/27
Non-ribosomal peptide synthetase modules and related proteins cog 0.00e+00 0.00e+00 4/27
Polyketide synthase modules and related proteins cog 0.00e+00 0.00e+00 5/27
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 306

There are 27 genes in Module 306

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU02310 ybfO CDS None chromosome 249967 251307 + putative exported hydrolase (RefSeq) False
BSU12460 xlyB CDS None chromosome 1316849 1317802 + N-acetylmuramoyl-L-alanine amidase; bacteriophage PBSX protein (RefSeq) False
BSU15300 bpr CDS None chromosome 1598580 1602881 + bacillopeptidase F (RefSeq) False
BSU17120 pksE CDS None chromosome 1785290 1787593 + enzyme involved in polyketide synthesis (RefSeq) False
BSU17130 acpK CDS None chromosome 1787654 1787902 + acyl carrier protein (RefSeq) False
BSU17140 pksF CDS None chromosome 1787880 1789130 + polyketide beta-ketoacyl:acyl carrier protein synthase (RefSeq) False
BSU17150 pksG CDS None chromosome 1789131 1790393 + acetyl-S-AcpK beta-ketothioester polyketide intermediate transferase (RefSeq) False
BSU17160 pksH CDS None chromosome 1790381 1791160 + polyketide biosynthesis enoyl-CoA hydratase (RefSeq) False
BSU17170 pksI CDS None chromosome 1791200 1791949 + polyketide biosynthesis enoyl-CoA hydratase (RefSeq) False
BSU17180 pksJ CDS None chromosome 1791994 1807131 + polyketide synthase of type I (RefSeq) False
BSU17190 pksL CDS None chromosome 1807115 1820731 + polyketide synthase of type I (RefSeq) False
BSU17200 pksM CDS None chromosome 1820747 1833535 + polyketide synthase (RefSeq) False
BSU17210 pksN CDS None chromosome 1833603 1850069 + polyketide synthase of type I (RefSeq) False
BSU17220 pksR CDS None chromosome 1850084 1857715 + polyketide synthase (RefSeq) False
BSU18310 ppsD CDS None chromosome 1963254 1974065 - plipastatin synthetase (RefSeq) False
BSU18320 ppsC CDS None chromosome 1974090 1981757 - plipastatin synthetase (RefSeq) False
BSU18330 ppsB CDS None chromosome 1981774 1989456 - plipastatin synthetase (RefSeq) False
BSU18340 ppsA CDS None chromosome 1989481 1997166 - plipastatin synthetase (RefSeq) False
BSU21440 bdbB CDS None chromosome 2264421 2264867 - bacteriophage SPbeta thiol-disulfide oxidoreductase (RefSeq) False
BSU21450 yolJ CDS None chromosome 2264864 2266132 - putative glycosyltransferase (RefSeq) False
BSU21460 bdbA CDS None chromosome 2266132 2266545 - bacteriophage SPbeta thiol-disulfide oxidoreductase (RefSeq) False
BSU21470 sunT CDS None chromosome 2266542 2268659 - sublancin 168 lantibiotic transporter (RefSeq) False
BSU23480 dacF CDS None chromosome 2444283 2445452 - D-alanyl-D-alanine carboxypeptidase (penicilin binding protein) (RefSeq) False
BSU33750 sdpA CDS None chromosome 3463320 3463796 + export of killing factor (RefSeq) False
BSU33760 sdpB CDS None chromosome 3463793 3464764 + exporter of killing factor SpbC (RefSeq) False
BSU40160 yydH CDS None chromosome 4124766 4125524 - putative membrane metalloprotease (RefSeq) False
BSU40170 yydG CDS None chromosome 4125505 4126464 - putative AdoMet radical enzyme (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 306

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.