Organism : Bacillus subtilis | Module List:
Module 340 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 340

There are 15 regulatory influences for Module 340

Regulator Table (15)
Regulator Name Type
BSU23120 tf
BSU16900 tf
BSU00700 tf
BSU29110 tf
BSU02680 tf
BSU15880 tf
BSU14140 tf
BSU09990 tf
BSU27110 tf
BSU03620 tf
BSU09270 tf
BSU05580 tf
BSU39430 tf
BSU40960 tf
BSU13340 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
5614 4.70e-01 GCttTTtTT.t
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5615 3.30e+01 aaAtGaagG.agggg
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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 340 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 1.52e-02 3.16e-02 4/27
Amino Acid Metabolism kegg subcategory 2.04e-03 8.42e-03 5/27
Valine leucine and isoleucine degradation kegg pathway 0.00e+00 1.00e-06 5/27
Signal Transduction kegg subcategory 6.47e-04 3.88e-03 4/27
Two-component system kegg pathway 6.47e-04 3.88e-03 4/27
Global kegg category 1.27e-02 2.79e-02 8/27
Metabolism kegg subcategory 1.27e-02 2.79e-02 8/27
Metabolic pathways kegg pathway 8.31e-03 2.03e-02 8/27
Biosynthesis of secondary metabolites kegg pathway 7.19e-03 1.84e-02 5/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 1.82e-02 2.85e-02 3/27
Posttranslational modification, protein turnover, chaperones cog subcategory 3.58e-03 6.04e-03 3/27
Energy production and conversion cog subcategory 1.09e-04 2.52e-04 6/27
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 340

There are 27 genes in Module 340

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU06240 test CDS None chromosome 677459 678499 - acetoin reductase/2,3-butanediol dehydrogenase (RefSeq) False
BSU06850 yeeK CDS None chromosome 752602 753039 + spore associated protein (RefSeq) False
BSU10850 yisS CDS None chromosome 1163675 1164703 + putative dehydrogenase (RefSeq) False
BSU16980 spoVS CDS None chromosome 1769205 1769465 + regulator required for dehydratation of the spore core and assembly of the coat (stage V sporulation) (RefSeq) False
BSU22570 ypiF CDS None chromosome 2364431 2364877 - hypothetical protein (RefSeq) False
BSU22580 ypiB CDS None chromosome 2364932 2365471 - hypothetical protein (RefSeq) False
BSU22590 ypiA CDS None chromosome 2365543 2366814 - hypothetical protein (RefSeq) False
BSU23110 resE CDS None chromosome 2414609 2416378 - two-component sensor histidine kinase (RefSeq) False
BSU23120 resD CDS None chromosome 2416375 2417097 - two-component response regulator (RefSeq) True
BSU23130 resC CDS None chromosome 2417178 2418236 - factor required for cytochrome c synthesis (RefSeq) False
BSU23140 resB CDS None chromosome 2418372 2420000 - factor required for cytochrome c synthesis (RefSeq) False
BSU23150 resA CDS None chromosome 2419997 2420542 - thiol-disulfide oxidoreductase (RefSeq) False
BSU24030 bkdB CDS None chromosome 2495987 2497261 - branched-chain alpha-keto acid dehydrogenase subunit E2 (RefSeq) False
BSU24040 bkdAB CDS None chromosome 2497284 2498267 - branched-chain alpha-keto acid dehydrogenase E1 subunit (RefSeq) False
BSU24050 bkdAA CDS None chromosome 2498281 2499273 - branched-chain alpha-keto acid dehydrogenase E1 subunit (RefSeq) False
BSU24060 lpdV CDS None chromosome 2499347 2500720 - dihydrolipoamide dehydrogenase (RefSeq) False
BSU24070 buk CDS None chromosome 2500741 2501832 - butyrate kinase (RefSeq) False
BSU24080 bcd CDS None chromosome 2501851 2502945 - branched-chain amino acid dehydrogenase (RefSeq) False
BSU24090 ptb CDS None chromosome 2502957 2503856 - phosphate butyryltransferase (RefSeq) False
BSU27220 yrhE CDS None chromosome 2780436 2783378 + putative oxido-reductase (RefSeq) False
BSU27230 yrhD CDS None chromosome 2783397 2783879 + hypothetical protein (RefSeq) False
BSU29670 tyrS CDS None chromosome 3035645 3036913 - tyrosyl-tRNA synthetase (RefSeq) False
BSU29890 ytnP CDS None chromosome 3057680 3058450 - putative metal-dependent hydrolase (RefSeq) False
BSU30660 ytkA CDS None chromosome 3135986 3136423 - putative lipoprotein (RefSeq) False
BSU31690 comP CDS None chromosome 3252573 3254882 - two-component sensor histidine kinase (RefSeq) False
BSU31700 comX CDS None chromosome 3254897 3255064 - competence pheromone precursor (pheromone peptide aa 46->55, modified) (RefSeq) False
BSU39430 deoR CDS None chromosome 4051396 4052337 - transcriptional regulator (RefSeq) True

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.