Organism : Bacillus subtilis | Module List:
Module 273 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 273

There are 9 regulatory influences for Module 273

Regulator Table (9)
Regulator Name Type
BSU25250 tf
BSU16900 tf
BSU05850 tf
BSU15880 tf
BSU16170 tf
BSU29740 tf
BSU01430 tf
BSU23210 tf
BSU01810 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
5484 1.50e+03 GAcAGAAa
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5485 1.80e+02 aaGGgaGGaga
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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 273 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 4.83e-03 1.41e-02 9/24
Carbohydrate Metabolism kegg subcategory 2.33e-04 1.83e-03 6/24
Pentose phosphate pathway kegg pathway 1.00e-05 1.53e-04 3/24
Pyruvate metabolism kegg pathway 8.50e-05 8.62e-04 3/24
Lipid Metabolism kegg subcategory 3.20e-05 4.00e-04 4/24
Fatty acid biosynthesis kegg pathway 0.00e+00 0.00e+00 4/24
Global kegg category 5.36e-03 1.51e-02 8/24
Metabolism kegg subcategory 5.36e-03 1.51e-02 8/24
Metabolic pathways kegg pathway 3.41e-03 1.13e-02 8/24
Biosynthesis of secondary metabolites kegg pathway 6.68e-04 3.96e-03 6/24
Microbial metabolism in diverse environments kegg pathway 1.58e-02 3.26e-02 3/24

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 4.07e-03 5.91e-03 3/24
Fatty acid and phospholipid metabolism tigr mainrole 0.00e+00 0.00e+00 5/24
Biosynthesis tigr sub1role 0.00e+00 0.00e+00 5/24
Protein fate tigr mainrole 4.43e-04 7.85e-04 3/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 1.64e-02 2.58e-02 8/24
Carbohydrate transport and metabolism cog subcategory 2.03e-02 3.14e-02 4/24
Lipid transport and metabolism cog subcategory 3.00e-05 9.00e-05 5/24
Function unknown cog subcategory 2.10e-03 3.64e-03 6/24
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 273

There are 24 genes in Module 273

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU00370 abrB CDS None chromosome 44846 45136 - transcriptional regulator for transition state genes (RefSeq) True
BSU15260 ylxX CDS None chromosome 1594508 1595215 + hypothetical protein (RefSeq) False
BSU15270 sbp CDS None chromosome 1595233 1595598 + putative integral inner membrane protein (RefSeq) False
BSU15400 ylmG CDS None chromosome 1610624 1610896 + factor involved in shape determination (RefSeq) False
BSU15900 fabD CDS None chromosome 1662867 1663820 + malonyl CoA:acyl carrier protein transacylase (RefSeq) False
BSU15910 fabG CDS None chromosome 1663813 1664553 + beta-ketoacyl-acyl carrier protein reductase (RefSeq) False
BSU15920 acpP CDS None chromosome 1664637 1664870 + acyl carrier protein (RefSeq) False
BSU16150 clpQ CDS None chromosome 1687414 1687959 + ATP-dependent protease peptidase subunit (RefSeq) False
BSU16160 hslU CDS None chromosome 1687976 1689379 + ATP-dependent protease ATP-binding subunit HslU (RefSeq) False
BSU16660 truB CDS None chromosome 1736178 1737107 + tRNA pseudouridine synthase B (RefSeq) False
BSU17890 tkt CDS None chromosome 1919070 1921073 + transketolase (RefSeq) False
BSU23500 drm CDS None chromosome 2446435 2447619 - phosphopentomutase (RefSeq) False
BSU23910 yqjE CDS None chromosome 2484867 2485982 - putative deacylase (RefSeq) False
BSU24330 yqhY CDS None chromosome 2529157 2529564 - hypothetical protein (RefSeq) False
BSU24340 accC CDS None chromosome 2529585 2530937 - acetyl-CoA carboxylase biotin carboxylase subunit (RefSeq) False
BSU24350 accB CDS None chromosome 2530949 2531428 - acetyl-CoA carboxylase biotin carboxyl carrier protein subunit (RefSeq) False
BSU25240 yqfL CDS None chromosome 2603354 2604166 - hypothetical protein (RefSeq) False
BSU25250 ccpN CDS None chromosome 2604192 2604830 - negative regulator of gluconeogenesis (RefSeq) True
BSU27650 secDF CDS None chromosome 2826126 2828339 - bifunctional preprotein translocase subunit SecD/SecF (RefSeq) False
BSU29180 pyk CDS None chromosome 2983827 2985584 - pyruvate kinase (RefSeq) False
BSU30800 menB CDS None chromosome 3147949 3148764 - naphthoate synthase (RefSeq) False
BSU34800 cwlO CDS None chromosome 3573393 3574814 - secreted cell wall DL-endopeptidase (RefSeq) False
BSU37090 glpX CDS None chromosome 3804113 3805078 - fructose 1,6-bisphosphatase II (RefSeq) False
BSU38540 dltE CDS None chromosome 3955513 3956271 + putative oxidoreductase (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 273

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.