Organism : Bacillus subtilis | Module List:
Module 28 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 28

There are 12 regulatory influences for Module 28

Regulator Table (12)
Regulator Name Type
BSU33840 tf
BSU04060 tf
BSU05330 tf
BSU07220 tf
BSU37550 tf
BSU06580 tf
BSU19050 tf
BSU10830 tf
BSU13150 tf
BSU08520 tf
BSU09270 tf
BSU04100 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
5016 6.40e-12 agaA.gGTGCtAAaTCcatcAag
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5017 2.80e-02 tcTggaAGATaAGa
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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 28 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 0.00e+00 21/28
Energy Metabolism kegg subcategory 1.36e-04 1.22e-03 5/28
Methane metabolism kegg pathway 4.10e-05 4.88e-04 3/28
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 18/28
Cysteine and methionine metabolism kegg pathway 0.00e+00 0.00e+00 11/28
Arginine and proline metabolism kegg pathway 2.28e-04 1.80e-03 3/28
Global kegg category 0.00e+00 0.00e+00 21/28
Metabolism kegg subcategory 0.00e+00 0.00e+00 21/28
Metabolic pathways kegg pathway 0.00e+00 0.00e+00 20/28
Biosynthesis of secondary metabolites kegg pathway 1.00e-06 1.40e-05 10/28
Microbial metabolism in diverse environments kegg pathway 2.68e-02 4.91e-02 3/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid biosynthesis tigr mainrole 0.00e+00 0.00e+00 6/28
Aspartate family tigr sub1role 4.00e-06 1.00e-05 3/28

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 23/28
Carbohydrate transport and metabolism cog subcategory 2.11e-03 3.65e-03 6/28
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 16/28
Methionine synthase II (cobalamin-independent) cog 0.00e+00 0.00e+00 3/28
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 28

There are 28 genes in Module 28

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU06040 ydiM CDS None chromosome 652979 653359 + hypothetical protein (RefSeq) False
BSU10340 phoE CDS None chromosome 1108040 1108621 - phosphatase (RefSeq) False
BSU11010 yitJ CDS None chromosome 1178062 1179900 - bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein (RefSeq) False
BSU11210 argB CDS None chromosome 1196633 1197409 + acetylglutamate kinase (RefSeq) False
BSU11220 argD CDS None chromosome 1197406 1198563 + acetylornithine aminotransferase (RefSeq) False
BSU11230 carA CDS None chromosome 1198634 1199695 + carbamoyl phosphate synthase small subunit (RefSeq) False
BSU11240 carB CDS None chromosome 1199688 1202780 + carbamoyl phosphate synthase large subunit (RefSeq) False
BSU11250 argF CDS None chromosome 1202768 1203727 + ornithine carbamoyltransferase (RefSeq) False
BSU11870 yjcI CDS None chromosome 1257804 1258925 + cystathionine gamma-synthase (RefSeq) False
BSU11880 yjcJ CDS None chromosome 1258918 1260090 + cystathionine beta-lyase (RefSeq) False
BSU13180 metE CDS None chromosome 1382626 1384914 - 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase (RefSeq) False
BSU13550 mtnA CDS None chromosome 1421480 1422541 - methylthioribose-1-phosphate isomerase (RefSeq) False
BSU13560 mtnK CDS None chromosome 1422549 1423748 - methylthioribose kinase (RefSeq) False
BSU13580 ykrV CDS None chromosome 1424949 1426145 + transaminase (RefSeq) False
BSU13590 mtnW CDS None chromosome 1426342 1427586 + 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (RefSeq) False
BSU13600 mtnX CDS None chromosome 1427583 1428290 + 2-hydroxy-3-keto-5-methylthiopentenyl-1- phosphate phosphatase (RefSeq) False
BSU13610 mtnB CDS None chromosome 1428248 1428877 + methylthioribulose-1-phosphate dehydratase (RefSeq) False
BSU13620 mtnD CDS None chromosome 1428892 1429428 + acireductone dioxygenase (Ni2+ or Fe2+-requiring) (RefSeq) False
BSU18540 yoaB CDS None chromosome 2020433 2021677 - negatively charged metabolite transporter (RefSeq) False
BSU18550 yoaC CDS None chromosome 2021771 2023234 - hydroxylated metabolite kinase (RefSeq) False
BSU18560 yoaD CDS None chromosome 2023252 2024286 - putative 2-hydroxyacid dehydrogenase (RefSeq) False
BSU18570 yoaE CDS None chromosome 2024610 2026643 + molybdopterin cofactor oxido-reductase (RefSeq) False
BSU18580 yoaF CDS None chromosome 2026720 2027013 + hypothetical protein (RefSeq) False
BSU19580 yodF CDS None chromosome 2129576 2131066 + putative Na+/metabolite permease (RefSeq) False
BSU21870 ilvD CDS None chromosome 2299958 2301634 - dihydroxy-acid dehydratase (RefSeq) False
BSU26760 yrdC CDS None chromosome 2732206 2732769 - putative hydrolase (RefSeq) False
BSU38950 yxjH CDS None chromosome 3996983 3998005 + putative methyl-tetrahydrofolate methyltransferase (RefSeq) False
BSU38960 yxjG CDS None chromosome 3998368 3999504 + putative methyltetrahydrofolate methyltransferase (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 28

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.