Organism : Bacillus subtilis | Module List:
Module 247 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 247

There are 17 regulatory influences for Module 247

Regulator Table (17)
Regulator Name Type
BSU28820 tf
BSU29000 tf
BSU35650 tf
BSU19120 tf
BSU01810 tf
BSU40010 tf
BSU38220 tf
BSU04650 tf
BSU38910 tf
BSU09990 tf
BSU25760 tf
BSU25250 tf
BSU16900 tf
BSU33970 tf
BSU33840 tf
BSU04680 tf
BSU23090 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
5436 3.90e+00 aGCtGGcatAgGCaG
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5437 5.20e+01 AaAAAGaaTgcA.gagTgATGA
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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 247 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 7.34e-03 1.87e-02 10/29
Carbohydrate Metabolism kegg subcategory 1.27e-04 1.16e-03 7/29
Glycolysis / Gluconeogenesis kegg pathway 8.00e-06 1.18e-04 4/29
Pentose phosphate pathway kegg pathway 2.20e-05 2.98e-04 3/29
Pyruvate metabolism kegg pathway 1.83e-04 1.54e-03 3/29
Energy Metabolism kegg subcategory 1.45e-03 6.75e-03 4/29
Methane metabolism kegg pathway 4.80e-05 5.50e-04 3/29
Amino Acid Metabolism kegg subcategory 1.48e-02 3.11e-02 4/29
Global kegg category 2.07e-02 4.01e-02 8/29
Metabolism kegg subcategory 2.07e-02 4.01e-02 8/29
Metabolic pathways kegg pathway 1.37e-02 2.95e-02 8/29
Biosynthesis of secondary metabolites kegg pathway 2.26e-03 8.93e-03 6/29
Microbial metabolism in diverse environments kegg pathway 1.00e-06 2.70e-05 8/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 1.21e-04 2.42e-04 5/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.29e-02 2.05e-02 14/29
Poorly characterized cog category 2.26e-03 3.92e-03 11/29
Energy production and conversion cog subcategory 7.38e-03 1.21e-02 4/29
General function prediction only cog subcategory 1.72e-02 2.69e-02 6/29
Function unknown cog subcategory 2.49e-02 3.81e-02 5/29
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 247

There are 29 genes in Module 247

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU04040 ycsE CDS None chromosome 455622 456371 + putative phosphatase (RefSeq) False
BSU09570 yhdR CDS None chromosome 1033354 1034535 + aspartate aminotransferase (RefSeq) False
BSU10020 serC CDS None chromosome 1074594 1075673 - phosphoserine aminotransferase (RefSeq) False
BSU11030 yitL CDS None chromosome 1180804 1181700 + putative RNA-binding protein (RefSeq) False
BSU14500 ykqA CDS None chromosome 1518942 1519775 + hypothetical protein (RefSeq) False
BSU14580 pdhA CDS None chromosome 1527633 1528748 + pyruvate dehydrogenase (E1 alpha subunit) (RefSeq) False
BSU14590 pdhB CDS None chromosome 1528752 1529729 + pyruvate dehydrogenase (E1 beta subunit) (RefSeq) False
BSU24450 efp CDS None chromosome 2537347 2537904 - elongation factor P (RefSeq) False
BSU24460 yqhT CDS None chromosome 2537929 2538990 - putative aminopeptidase (RefSeq) False
BSU24820 yqgU CDS None chromosome 2565470 2566531 - putative lipoprotein (RefSeq) False
BSU28820 ysdC CDS None chromosome 2949295 2950380 - putative endo-1,4-beta-glucanase (RefSeq) True
BSU31170 yulF CDS None chromosome 3195945 3196931 + enzyme involved in biofilm formation (RefSeq) False
BSU31350 pgi CDS None chromosome 3219769 3221124 - glucose-6-phosphate isomerase (RefSeq) False
BSU31740 yuxH CDS None chromosome 3257081 3258310 - putative phosphodiesterase (RefSeq) False
BSU31760 pncA CDS None chromosome 3259935 3260486 - nicotinamidase (RefSeq) False
BSU32300 yutE CDS None chromosome 3317854 3318288 - hypothetical protein (RefSeq) False
BSU32310 yutD CDS None chromosome 3318312 3318620 - hypothetical protein (RefSeq) False
BSU32800 yusH CDS None chromosome 3365150 3365533 - glycine cleavage system protein H (RefSeq) False
BSU33210 yvrG CDS None chromosome 3405640 3407361 - two-component sensor histidine kinase YvrG innvolved in cell wall processes [YvrH] (RefSeq) False
BSU34020 yvbX CDS None chromosome 3490686 3491720 - putative epimerase modification of peptidoglycan (RefSeq) False
BSU34640 yvdD CDS None chromosome 3557970 3558545 - hypothetical protein (RefSeq) False
BSU34650 yvdC CDS None chromosome 3558662 3558982 + putative pyrophosphohydrolase (RefSeq) False
BSU35850 ywtE CDS None chromosome 3694390 3695250 + putative hydrolase (RefSeq) False
BSU37110 ywjH CDS None chromosome 3806777 3807415 - putative translaldolase (RefSeq) False
BSU37120 fbaA CDS None chromosome 3807535 3808392 - fructose-bisphosphate aldolase (RefSeq) False
BSU37340 ywiB CDS None chromosome 3834340 3834768 - hypothetical protein (RefSeq) False
BSU37660 eutD CDS None chromosome 3864377 3865348 - phosphotransacetylase (RefSeq) False
BSU38210 ywcD CDS None chromosome 3920914 3921297 - putative integral inner membrane protein (RefSeq) False
BSU40550 ppaC CDS None chromosome 4167228 4168157 + putative manganese-dependent inorganic pyrophosphatase (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.