Organism : Bacillus subtilis | Module List:
Module 101 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 101

There are 14 regulatory influences for Module 101

Regulator Table (14)
Regulator Name Type
BSU09990 tf
BSU10860 tf
BSU04680 tf
BSU36020 tf
BSU38600 tf
BSU10420 tf
BSU34170 tf
BSU35490 tf
BSU23450 tf
BSU05640 tf
BSU37080 tf
BSU29630 tf
BSU20780 tf
BSU08300 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
5156 4.00e-05 aaAAAGaggGg
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5157 1.90e+02 gCcTtcCtcttgttA
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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 101 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Nucleotide Metabolism kegg subcategory 2.99e-03 1.04e-02 3/26
Purine metabolism kegg pathway 9.03e-04 4.90e-03 3/26
Amino Acid Metabolism kegg subcategory 9.26e-03 2.19e-02 4/26
Arginine and proline metabolism kegg pathway 8.00e-06 1.19e-04 4/26
Microbial metabolism in diverse environments kegg pathway 3.73e-03 1.20e-02 4/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Central intermediary metabolism tigr mainrole 2.30e-05 5.60e-05 3/26
Nitrogen metabolism tigr sub1role 0.00e+00 0.00e+00 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 1.09e-02 1.75e-02 5/26
General function prediction only cog subcategory 3.30e-02 4.95e-02 5/26
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 101

There are 26 genes in Module 101

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU02820 rapJ CDS None chromosome 303982 305103 + response regulator aspartate phosphatase (RefSeq) False
BSU03010 amhX CDS None chromosome 323571 324740 - amidohydrolase (RefSeq) False
BSU04130 yczJ CDS None chromosome 463053 463340 - hypothetical protein (RefSeq) False
BSU04210 ydaF CDS None chromosome 472731 473282 + putative ribosomal protein N-acetyltransferase (RefSeq) False
BSU09670 dat CDS None chromosome 1041302 1042150 + D-alanine aminotransferase (RefSeq) False
BSU09990 hpr CDS None chromosome 1072413 1073024 - transcriptional regulator Hpr (RefSeq) True
BSU10070 yhaA CDS None chromosome 1079455 1080645 - putative amidohydrolase (RefSeq) False
BSU10200 yhfE CDS None chromosome 1094367 1095407 + putative endoglucanase (RefSeq) False
BSU10210 yhfF CDS None chromosome 1095420 1095827 + hypothetical protein (RefSeq) False
BSU10860 yisT CDS None chromosome 1164754 1165263 - hypothetical protein (RefSeq) True
BSU11840 yjcF CDS None chromosome 1255748 1256170 - putative acetyltransferase (RefSeq) False
BSU11850 yjcG CDS None chromosome 1256174 1256689 - hypothetical protein (RefSeq) False
BSU11860 yjcH CDS None chromosome 1256726 1257448 - putative hydrolase (RefSeq) False
BSU12210 yjiB CDS None chromosome 1290654 1291844 + putative monooxygenase (cytochrome P450) (RefSeq) False
BSU12220 yjiC CDS None chromosome 1291867 1293045 + putative glycosyltransferase (RefSeq) False
BSU32080 yuiB CDS None chromosome 3298369 3298689 - hypothetical protein (RefSeq) False
BSU32090 yuiA CDS None chromosome 3298743 3298886 - hypothetical protein (RefSeq) False
BSU36520 glnK CDS None chromosome 3757038 3757388 + nitrogen-regulated PII-like regulator protein (RefSeq) False
BSU36640 ureC CDS None chromosome 3765736 3767445 - urease subunit alpha (RefSeq) False
BSU36650 ureB CDS None chromosome 3767442 3767816 - urease (beta subunit) (RefSeq) False
BSU36660 ureA CDS None chromosome 3767813 3768130 - urease subunit gamma (RefSeq) False
BSU38090 vpr CDS None chromosome 3906867 3909287 + extracellular serine protease (RefSeq) False
BSU38470 ywaD CDS None chromosome 3947576 3948943 + double-zinc aminopeptidase (RefSeq) False
BSU40300 rapG CDS None chromosome 4139285 4140382 + response regulator aspartate phosphatase (RefSeq) False
BSU40310 phrG CDS None chromosome 4140383 4140499 + secreted regulator of the activity of phosphatase RapG (RefSeq) False
VIMSS37491 VIMSS37491 DUMMY None chromosome 0 0 + None 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.