Organism : Bacillus subtilis | Module List:
Module 96 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 96

There are 20 regulatory influences for Module 96

Regulator Table (20)
Regulator Name Type
BSU34380 tf
BSU08340 tf
BSU40410 tf
BSU33650 tf
BSU02890 tf
BSU34060 tf
BSU27170 tf
BSU12560 tf
BSU19090 tf
BSU25250 tf
BSU16900 tf
BSU03880 tf
BSU09480 tf
BSU33030 tf
BSU05170 tf
BSU33740 tf
BSU04680 tf
BSU25760 tf
BSU04730 tf
BSU26430 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
5146 2.50e+00 TgaccccctctTgtt
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5147 2.60e+02 ggCttcTTttT
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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 96 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Signal Transduction kegg subcategory 7.01e-03 1.80e-02 3/29
Two-component system kegg pathway 7.01e-03 1.80e-02 3/29

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 96

There are 29 genes in Module 96

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU02710 yczC CDS None chromosome 292433 292816 - putative integral inner membrane protein (RefSeq) False
BSU03110 ycgH CDS None chromosome 335684 336817 - putative amino acid transporter (RefSeq) False
BSU10470 yhjD CDS None chromosome 1120340 1120702 - hypothetical protein (RefSeq) False
BSU12080 ctaO CDS None chromosome 1278825 1279814 - protoheme IX farnesyltransferase (heme O synthase) (RefSeq) False
BSU12500 xkdA CDS None chromosome 1319881 1320477 - PBSX phage protein, putative peptidase (RefSeq) False
BSU13400 ligD CDS None chromosome 1403826 1405661 - ATP-dependent DNA ligase (RefSeq) False
BSU13410 ykoV CDS None chromosome 1405665 1406600 - ATP-dependent DNA ligase subunit (RefSeq) False
BSU16110 dprA CDS None chromosome 1681880 1682773 + DNA processing Smf single strand binding protein (RefSeq) False
BSU18710 yozF CDS None chromosome 2040786 2041037 - putative lipoprotein (RefSeq) False
BSU18720 yoaR CDS None chromosome 2041138 2042049 - putative factor for cell wall maintenance or synthesis (RefSeq) False
BSU18770 cyeA CDS None chromosome 2045139 2046017 + cysteine and O-acetyl serine efflux permease (RefSeq) False
BSU21940 degR CDS None chromosome 2307354 2307536 - activation of degradative enzymes (aprE, nprE, sacB) production or activity (RefSeq) False
BSU24910 yqgM CDS None chromosome 2573873 2574952 - putative glycosyltransferase (RefSeq) False
BSU24920 yqgL CDS None chromosome 2574949 2575419 - hypothetical protein (RefSeq) False
BSU26120 yqbG CDS None chromosome 2681712 2682107 - conserved hypothetical protein; skin element (RefSeq) False
BSU28900 ysbB CDS None chromosome 2953533 2954228 - antiholin-like protein LrgB (RefSeq) False
BSU28910 ysbA CDS None chromosome 2954250 2954690 - murein hydrolase regulator LrgA (RefSeq) False
BSU31420 yugF CDS None chromosome 3226622 3227443 + putative hydrolase (RefSeq) False
BSU31430 yugE CDS None chromosome 3227472 3227738 - hypothetical protein (RefSeq) False
BSU32020 yuiH CDS None chromosome 3292598 3293194 - putative sulfite oxidase (RefSeq) False
BSU32190 yuzB CDS None chromosome 3307393 3307629 - hypothetical protein (RefSeq) False
BSU33050 gerAA CDS None chromosome 3389809 3391257 + component of the GerA germination receptor (RefSeq) False
BSU33060 gerAB CDS None chromosome 3391226 3392323 + component of the germination receptor GerA (RefSeq) False
BSU33070 gerAC CDS None chromosome 3392320 3393441 + component of the germination receptor GerA (RefSeq) False
BSU33690 yvaQ CDS None chromosome 3457097 3458797 + putative methyl-accepting transducer (RefSeq) False
BSU34000 cyeB CDS None chromosome 3487983 3488900 + cysteine and O-acetylserine efflux permease (RefSeq) False
BSU38250 ywbO CDS None chromosome 3924819 3925421 - putative sulfur oxido-reductase (RefSeq) False
BSU38800 yxkH CDS None chromosome 3982206 3983045 - putative exported polysaccharide deacetylase, lipoprotein (RefSeq) False
BSU40530 cotF CDS None chromosome 4166134 4166616 + spore coat protein (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 96

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.