Organism : Bacillus subtilis | Module List:
Module 310 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 310

There are 13 regulatory influences for Module 310

Regulator Table (13)
Regulator Name Type
BSU33010 tf
BSU05270 tf
BSU08520 tf
BSU40710 tf
BSU24220 tf
BSU14240 tf
BSU24020 tf
BSU10860 tf
BSU05460 tf
BSU09650 tf
BSU25100 tf
BSU05700 tf
BSU05850 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
5558 5.20e-01 TATcATAAAaaaaaa
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5559 3.60e+00 at.aa..gag.aA.GgAGgga
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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 310 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Environmental Information Processing kegg category 1.09e-02 2.48e-02 5/29
Signal Transduction kegg subcategory 9.12e-04 4.93e-03 4/29
Two-component system kegg pathway 9.12e-04 4.93e-03 4/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Unknown function tigr mainrole 3.59e-03 5.27e-03 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 4.38e-03 7.35e-03 9/29
Signal transduction mechanisms cog subcategory 8.00e-06 3.10e-05 7/29
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 310

There are 29 genes in Module 310

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU03230 ycgP CDS None chromosome 348284 349519 + putative transcriptional regulator (RefSeq) False
BSU04130 yczJ CDS None chromosome 463053 463340 - hypothetical protein (RefSeq) False
BSU04990 yddJ CDS None chromosome 545156 545536 + putative lipoprotein (RefSeq) False
BSU05980 tatAY CDS None chromosome 647307 647480 + component of the twin-arginine pre-protein translocation pathway (RefSeq) False
BSU07640 yflL CDS None chromosome 837072 837347 - acylphosphatase (RefSeq) False
BSU10520 glcP CDS None chromosome 1124427 1125632 - glucose/mannose:H+ symporter (RefSeq) False
BSU10530 ntdC CDS None chromosome 1125704 1126756 - biosynthesis of neotrehalosadiamine (3,3'-diamino-3,3'-dideoxy-alpha,beta-trehalose), dehydrogenase (RefSeq) False
BSU10540 ntdB CDS None chromosome 1126759 1127619 - biosynthesis of neotrehalosadiamine (3,3'-diamino-3,3'-dideoxy-alpha,beta-trehalose); hydrolase (RefSeq) False
BSU10800 yizA CDS None chromosome 1158516 1158995 - hypothetical protein (RefSeq) False
BSU12900 htrA CDS None chromosome 1357243 1358592 - membrane bound serine protease Do, quality control protease (heat-shock protein) (RefSeq) False
BSU13660 kinD CDS None chromosome 1430794 1432314 - histidine kinase phosphorylating Spo0A (RefSeq) False
BSU14510 ktrC CDS None chromosome 1519838 1520503 + potassium uptake protein (RefSeq) False
BSU14840 ylaN CDS None chromosome 1551719 1552000 + hypothetical protein (RefSeq) False
BSU17630 yncC CDS None chromosome 1895632 1896891 + putative sugar transporter (RefSeq) False
BSU18400 yoeD CDS None chromosome 2003472 2003702 - putative excisionase (RefSeq) False
BSU18890 yobF CDS None chromosome 2057926 2058849 - hypothetical protein (RefSeq) False
BSU26470 yrkL CDS None chromosome 2707401 2707925 - putative NAD(P)H oxidoreductase (RefSeq) False
BSU26810 yrpC CDS None chromosome 2737534 2738331 + glutamate racemase (RefSeq) False
BSU27390 yrrK CDS None chromosome 2796626 2797042 - Holliday junction resolvase-like protein (RefSeq) False
BSU27400 yrzL CDS None chromosome 2797050 2797316 - hypothetical protein (RefSeq) False
BSU29650 ytrP CDS None chromosome 3032738 3034477 - putative diguanylate cyclase-related enzyme (RefSeq) False
BSU31920 yukF CDS None chromosome 3275976 3277280 + putative transcriptional regulator (RefSeq) False
BSU33010 cssR CDS None chromosome 3384751 3385428 + two-component response regulator (RefSeq) True
BSU33020 cssS CDS None chromosome 3385425 3386780 + two-component sensor histidine kinase (RefSeq) False
BSU35500 degS CDS None chromosome 3644409 3645566 - two-component sensor histidine kinase (RefSeq) False
BSU36330 ywpF CDS None chromosome 3740209 3740619 + hypothetical protein (RefSeq) False
BSU37750 ywfA CDS None chromosome 3873354 3874592 - putative efflux transporter (RefSeq) False
BSU40710 yybA CDS None chromosome 4182469 4182921 - putative transcriptional regulator (MarR family) (RefSeq) True
BSU40750 yyaQ CDS None chromosome 4185116 4185472 + 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.

Comments for Module 310

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.