Organism : Bacillus subtilis | Module List:
Module 188 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 188

There are 9 regulatory influences for Module 188

Regulator Table (9)
Regulator Name Type
BSU40410 tf
BSU00800 tf
BSU40990 tf
BSU27320 tf
BSU27080 tf
BSU05580 tf
BSU00700 tf
BSU04680 tf
BSU31530 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
5322 7.70e+03 AGGAgGAA
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5323 1.50e+04 GGcGGCC
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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 188 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 6.86e-04 4.02e-03 11/26
Metabolism of Cofactors and Vitamins kegg subcategory 0.00e+00 0.00e+00 8/26
Porphyrin and chlorophyll metabolism kegg pathway 0.00e+00 0.00e+00 7/26
Genetic Information Processing kegg category 7.89e-03 1.95e-02 4/26
Replication and Repair kegg subcategory 2.34e-04 1.84e-03 3/26
Signal Transduction kegg subcategory 4.69e-03 1.38e-02 3/26
Two-component system kegg pathway 4.69e-03 1.38e-02 3/26
Global kegg category 6.51e-04 3.89e-03 10/26
Metabolism kegg subcategory 6.51e-04 3.89e-03 10/26
Metabolic pathways kegg pathway 3.64e-04 2.53e-03 10/26
Biosynthesis of secondary metabolites kegg pathway 2.40e-05 3.19e-04 8/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA metabolism tigr mainrole 1.00e-03 1.64e-03 3/26
DNA replication, recombination, and repair tigr sub1role 6.85e-04 1.16e-03 3/26
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 1.00e-06 2.00e-06 6/26
Heme, porphyrin, and cobalamin tigr sub1role 0.00e+00 0.00e+00 5/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Replication, recombination and repair cog subcategory 1.19e-03 2.14e-03 4/26
Coenzyme transport and metabolism cog subcategory 0.00e+00 0.00e+00 8/26
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 188

There are 26 genes in Module 188

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU00200 yaaK CDS None chromosome 28527 28850 + hypothetical protein (RefSeq) False
BSU00210 recR CDS None chromosome 28865 29461 + recombination protein RecR (RefSeq) False
BSU00220 yaaL CDS None chromosome 29479 29703 + hypothetical protein (RefSeq) False
BSU10120 hemE CDS None chromosome 1085422 1086483 + uroporphyrinogen decarboxylase (RefSeq) False
BSU10130 hemH CDS None chromosome 1086555 1087487 + ferrochelatase (RefSeq) False
BSU10140 hemY CDS None chromosome 1087502 1088914 + protoporphyrinogen oxidase (RefSeq) False
BSU25000 pbpA CDS None chromosome 2581003 2583153 - transpeptidase (penicillin-binding protein 2A) (RefSeq) False
BSU28120 hemL CDS None chromosome 2871945 2873237 - glutamate-1-semialdehyde aminotransferase (RefSeq) False
BSU28130 hemB CDS None chromosome 2873267 2874241 - delta-aminolevulinic acid dehydratase (RefSeq) False
BSU28140 hemD CDS None chromosome 2874238 2875026 - uroporphyrinogen III cosynthase (RefSeq) False
BSU28150 hemC CDS None chromosome 2875016 2875960 - porphobilinogen deaminase (RefSeq) False
BSU28160 hemX CDS None chromosome 2875993 2876823 - negative effector of the concentration of glutamyl-tRNA reductase HemA (RefSeq) False
BSU29060 coaE CDS None chromosome 2969962 2970555 - dephospho-CoA kinase (RefSeq) False
BSU29070 ytaF CDS None chromosome 2970717 2971196 - putative integral inner membrane protein (RefSeq) False
BSU29080 mutM CDS None chromosome 2971368 2972204 - formamidopyrimidine-DNA glycosylase (RefSeq) False
BSU29090 polA CDS None chromosome 2972221 2974863 - DNA polymerase I (RefSeq) False
BSU29220 ytsJ CDS None chromosome 2988939 2990171 - NADP-dependent malic enzyme (conversion of malate into pyruvate) (RefSeq) False
BSU34730 yvcN CDS None chromosome 3567557 3568321 - putative acetyltransferase (RefSeq) False
BSU34740 crh CDS None chromosome 3568322 3568579 - phosphocarrier protein Chr (RefSeq) False
BSU34750 whiA CDS None chromosome 3568603 3569553 - putative morphogen (RefSeq) False
BSU34760 yvcK CDS None chromosome 3569576 3570529 - gluconeogenesis factor (RefSeq) False
BSU34770 yvcJ CDS None chromosome 3570531 3571418 - hypothetical protein (RefSeq) False
BSU34780 yvcI CDS None chromosome 3571443 3571919 - putative triphosphate pyrophosphate hydrolase (RefSeq) False
BSU40400 walK CDS None chromosome 4150876 4152711 - two-component sensor histidine kinase [YycF] (RefSeq) False
BSU40410 walR CDS None chromosome 4152719 4153426 - two-component response regulator [YycG] (RefSeq) True
BSU40500 rplI CDS None chromosome 4162221 4162670 - 50S ribosomal protein L9 (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 188

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.