Organism : Bacillus subtilis | Module List:
Module 326 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 326

There are 14 regulatory influences for Module 326

Regulator Table (14)
Regulator Name Type
BSU28410 tf
BSU02000 tf
BSU23090 tf
BSU05370 tf
BSU00370 tf
BSU17590 tf
BSU06960 tf
BSU07590 tf
BSU08100 tf
BSU39850 tf
BSU26320 tf
BSU23100 tf
BSU07010 tf
BSU09480 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
5590 3.80e-05 A.aAaaggGAGtTgaag
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5591 9.90e+01 AaGGAg
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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 326 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 2.71e-04 2.06e-03 11/24
Carbohydrate Metabolism kegg subcategory 9.15e-03 2.18e-02 4/24
Ascorbate and aldarate metabolism kegg pathway 0.00e+00 9.00e-06 3/24
Nucleotide Metabolism kegg subcategory 2.20e-03 8.85e-03 3/24
Purine metabolism kegg pathway 6.59e-04 3.91e-03 3/24
Amino Acid Metabolism kegg subcategory 1.06e-03 5.50e-03 5/24
Histidine metabolism kegg pathway 0.00e+00 0.00e+00 5/24
Global kegg category 2.79e-04 2.11e-03 10/24
Metabolism kegg subcategory 2.79e-04 2.11e-03 10/24
Metabolic pathways kegg pathway 1.53e-04 1.33e-03 10/24
Microbial metabolism in diverse environments kegg pathway 2.58e-03 9.63e-03 4/24

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
Amino acids and amines tigr sub1role 0.00e+00 0.00e+00 4/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 5.00e-05 1.30e-04 16/24
Energy production and conversion cog subcategory 3.15e-03 5.36e-03 4/24
Amino acid transport and metabolism cog subcategory 1.43e-03 2.54e-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 326

There are 24 genes in Module 326

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU02460 ycbC CDS None chromosome 267881 268807 + 5-dehydro-4-deoxyglucarate dehydratase (RefSeq) False
BSU02470 ycbD CDS None chromosome 268837 270303 + 2,5-dioxovalerate dehydrogenase (alpha-ketoglutaric semialdehyde dehydrogenase) (RefSeq) False
BSU02510 garD CDS None chromosome 274020 275552 + D-galactarate dehydratase (RefSeq) False
BSU05230 ydeK CDS None chromosome 569915 570778 - putative permease (RefSeq) False
BSU06150 gutB CDS None chromosome 667014 668075 + glucitol (sorbitol) dehydrogenase (RefSeq) False
BSU06160 gutP CDS None chromosome 668149 669540 + H+-glucitol symporter (RefSeq) False
BSU06300 cotA CDS None chromosome 683010 684551 - spore copper-dependent laccase (RefSeq) False
BSU10970 yitF CDS None chromosome 1174166 1175281 - putative enolase superfamily enzyme (RefSeq) False
BSU10980 yitG CDS None chromosome 1175290 1176558 - putative efflux transporter (RefSeq) False
BSU19510 yojB CDS None chromosome 2123728 2123964 - hypothetical protein (RefSeq) False
BSU19810 ypqP CDS None chromosome 2150824 2151249 + hypothetical protein (RefSeq) False
BSU20190 yosA CDS None chromosome 2169005 2169124 + hypothetical protein from phage SPbeta (RefSeq) False
BSU32470 pucE CDS None chromosome 3334777 3335298 - xanthine dehydrogenase, iron-sulfur subunit (RefSeq) False
BSU32480 pucD CDS None chromosome 3335289 3337526 - xanthine dehydrogenase, substrate and molybdenum cofactor subunit (RefSeq) False
BSU32490 pucC CDS None chromosome 3337527 3338360 - xanthine dehydrogenase, FAD-binding subunit (RefSeq) False
BSU34080 yvfS CDS None chromosome 3496645 3497382 - putative ABC transporter (permease) (RefSeq) False
BSU34090 yvfR CDS None chromosome 3497383 3498288 - putative ABC efflux transporter (ATP-binding protein) (RefSeq) False
BSU34530 cotR CDS None chromosome 3543672 3544634 + spore coat protein assembly factor CotR (RefSeq) False
BSU36030 ywrK CDS None chromosome 3711644 3712972 + putative Na+/H+ antiporter (RefSeq) False
BSU39350 hutH CDS None chromosome 4041069 4042595 + histidine ammonia-lyase (RefSeq) False
BSU39360 hutU CDS None chromosome 4042592 4044250 + urocanate hydratase (RefSeq) False
BSU39370 hutI CDS None chromosome 4044263 4045528 + imidazolonepropionase (RefSeq) False
BSU39380 hutG CDS None chromosome 4045521 4046480 + formimidoylglutamase (RefSeq) False
BSU39390 hutM CDS None chromosome 4046556 4047983 + histidine permease (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 326

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.