Organism : Bacillus subtilis | Module List:
Module 107 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 107

There are 12 regulatory influences for Module 107

Regulator Table (12)
Regulator Name Type
BSU03960 tf
BSU30460 tf
BSU11660 tf
BSU33030 tf
BSU34380 tf
BSU00800 tf
BSU36020 tf
BSU39770 tf
BSU03080 tf
BSU36300 tf
BSU35520 tf
BSU15880 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
5168 2.30e-01 AAaagGaggtGaaat
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5169 1.50e+03 GccCTtGTC
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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 107 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 0.00e+00 3.00e-06 15/24
Energy Metabolism kegg subcategory 5.85e-04 3.60e-03 4/24
Oxidative phosphorylation kegg pathway 1.00e-06 2.30e-05 4/24
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 11/24
Phenylalanine tyrosine and tryptophan biosynthesis kegg pathway 0.00e+00 0.00e+00 11/24
Environmental Information Processing kegg category 1.91e-02 3.78e-02 4/24
Membrane Transport kegg subcategory 2.51e-03 9.50e-03 4/24
ABC transporters kegg pathway 7.54e-04 4.28e-03 4/24
Global kegg category 0.00e+00 0.00e+00 15/24
Metabolism kegg subcategory 0.00e+00 0.00e+00 15/24
Metabolic pathways kegg pathway 0.00e+00 0.00e+00 15/24
Biosynthesis of secondary metabolites kegg pathway 0.00e+00 0.00e+00 11/24

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 4.46e-04 7.90e-04 4/24
Electron transport tigr sub1role 0.00e+00 0.00e+00 4/24
Amino acid biosynthesis tigr mainrole 0.00e+00 0.00e+00 8/24
Aromatic amino acid family tigr sub1role 0.00e+00 0.00e+00 7/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 0.00e+00 0.00e+00 20/24
Energy production and conversion cog subcategory 4.29e-04 8.44e-04 5/24
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 11/24
Inorganic ion transport and metabolism cog subcategory 3.15e-03 5.36e-03 4/24
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 107

There are 24 genes in Module 107

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU05480 ydfN CDS None chromosome 596022 596642 + putative oxidoreductase (RefSeq) False
BSU12260 yjlA CDS None chromosome 1295930 1296904 - putative permease (RefSeq) False
BSU16960 ymdA CDS None chromosome 1766580 1768142 + phosphodiesterase (RefSeq) False
BSU17790 yndH CDS None chromosome 1911548 1912165 + hypothetical protein (RefSeq) False
BSU22610 tyrA CDS None chromosome 2368447 2369562 - prephenate dehydrogenase (RefSeq) False
BSU22620 hisC CDS None chromosome 2369611 2370693 - histidinol-phosphate aminotransferase (RefSeq) False
BSU22630 trpA CDS None chromosome 2370704 2371507 - tryptophan synthase subunit alpha (RefSeq) False
BSU22640 trpB CDS None chromosome 2371500 2372702 - tryptophan synthase subunit beta (RefSeq) False
BSU22650 trpF CDS None chromosome 2372683 2373330 - N-(5'-phosphoribosyl)anthranilate isomerase (RefSeq) False
BSU22660 trpC CDS None chromosome 2373335 2374087 - indole-3-glycerol-phosphate synthase (RefSeq) False
BSU22670 trpD CDS None chromosome 2374080 2375096 - anthranilate phosphoribosyltransferase (RefSeq) False
BSU22680 trpE CDS None chromosome 2375068 2376615 - anthranilate synthase component I (RefSeq) False
BSU22690 aroH CDS None chromosome 2376831 2377214 - chorismate mutase (RefSeq) False
BSU22700 aroB CDS None chromosome 2377211 2378299 - 3-dehydroquinate synthase (RefSeq) False
BSU22710 aroF CDS None chromosome 2378361 2379470 - chorismate synthase (RefSeq) False
BSU30740 mntD CDS None chromosome 3141125 3142012 - manganese ABC transporter (permease) (RefSeq) False
BSU30750 mntC CDS None chromosome 3142002 3143309 - manganese ABC transporter (permease) (RefSeq) False
BSU30760 mntB CDS None chromosome 3143315 3144067 - manganese ABC transporter (ATP-binding protein) (RefSeq) False
BSU30770 mntA CDS None chromosome 3144086 3145006 - manganese ABC transporter (manganese binding lipoprotein) (RefSeq) False
BSU33480 bdbD CDS None chromosome 3437095 3437763 - thiol-disulfide oxidoreductase (RefSeq) False
BSU38140 qoxD CDS None chromosome 3913338 3913712 - cytochrome aa3-600 quinol oxidase (subunit IV) (RefSeq) False
BSU38150 qoxC CDS None chromosome 3913714 3914328 - cytochrome aa3-600 quinol oxidase (subunit III) (RefSeq) False
BSU38160 qoxB CDS None chromosome 3914342 3916291 - cytochrome aa3-600 quinol oxidase (subunit I) (RefSeq) False
BSU38170 qoxA CDS None chromosome 3916319 3917284 - cytochrome aa3-600 quinol oxidase (subunit II) (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.