Organism : Clostridium acetobutylicum | Module List:
Module 298 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 298

There are 9 regulatory influences for Module 298

Regulator Table (9)
Regulator Name Type
CAC0514 tf
CAC3729 tf
CAC2297 tf
CAC2209 tf
CAC2053 tf
CAC0707 tf
CAC3199 tf
CAC2851 tf
CAC0360 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
7248 3.20e-05 aaGGa.GAtA
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7249 5.60e+03 GaGGAGGtaAGCTaG
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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 298 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 8.61e-03 1.50e-02 9/27
Signal transduction mechanisms cog subcategory 2.61e-03 4.86e-03 5/27
Function unknown cog subcategory 2.84e-03 5.27e-03 6/27
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 298

There are 27 genes in Module 298

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0005 CAC0005 CDS None chromosome 4489 4821 + Uncharacterized small conserved protein, ortholog of YAAB B.subtilis (NCBI ptt file) False
CAC0034 CAC0034 CDS None chromosome 45291 45596 - Hypothetical protein (NCBI ptt file) False
CAC0277 CAC0277 CDS None chromosome 316245 317363 + HD-GYP hydrolase domain containing protein (NCBI ptt file) False
CAC0475 CAC0475 CDS None chromosome 548430 549485 + HD-GYP domain (NCBI ptt file) False
CAC0639 CAC0639 CDS None chromosome 744438 744710 + Flagellar biosynthesis related protein (NCBI ptt file) False
CAC0640 CAC0640 CDS None chromosome 744715 745410 + Predicted phoshohydrolase (NCBI ptt file) False
CAC0904 CAC0904 CDS None chromosome 1034477 1036735 - ATPase with chaperon activity, two ATP-binding domains, ClpC orthologs (NCBI ptt file) False
CAC0957 CAC0957 CDS None chromosome 1094974 1096278 + Xre family DNA-binding domain and TPR-repeat-containing protein (NCBI ptt file) False
CAC1414 CAC1414 CDS None chromosome 1560000 1560605 + TerE family protein, ortholog of stress responce protein SCP2 (YCEC) B.subtilis (NCBI ptt file) False
CAC1416 CAC1416 CDS None chromosome 1561646 1562161 + Predicted acetyltransferase (NCBI ptt file) False
CAC1485 CAC1485 CDS None chromosome 1631998 1634304 + Glycosyltransferase, involved in cell wall biogenesis (NCBI ptt file) False
CAC1579 CAC1579 CDS None chromosome 1722695 1724008 + Methyl-accepting chemotaxis-like protein (chemotaxis sensory transducer) (NCBI ptt file) False
CAC1604 CAC1604 CDS None chromosome 1747872 1748321 + Methylglyoxal synthase (NCBI ptt file) False
CAC1605 arbA CDS None chromosome 1748371 1749276 + Ketopantoate reductase (NCBI ptt file) False
CAC1623 CAC1623 CDS None chromosome 1762680 1763321 + Uncharacterized protein, ortholog of Thermotoga (4980645) (NCBI ptt file) False
CAC1624 CAC1624 CDS None chromosome 1763428 1764270 + Uncharacterized protein from DegV (B.subtilis) family (NCBI ptt file) False
CAC1840 CAC1840 CDS None chromosome 1992885 1993760 - Predicted acetyltransferase domain containing protein (NCBI ptt file) False
CAC2195 CAC2195 CDS None chromosome 2287501 2288805 - Protein containing aminopeptidase domain (NCBI ptt file) False
CAC2422 CAC2422 CDS None chromosome 2538897 2539769 - Oxygen-independent coproporphyrinogen III oxidase, Fe-S oxidoreductase (NCBI ptt file) False
CAC2677 CAC2677 CDS None chromosome 2795526 2796239 - Lytic murein transglycosylase (NCBI ptt file) False
CAC2714 CAC2714 CDS None chromosome 2837833 2839764 + ABC-type transporter, duplicate ATPase component (NCBI ptt file) False
CAC2726 CAC2726 CDS None chromosome 2851254 2851421 - Uncharacterized protein, possible ynzC B.subtilis homolog (NCBI ptt file) False
CAC2901 CAC2901 CDS None chromosome 3034752 3035558 - Predicted membrane protein (NCBI ptt file) False
CAC2904 CAC2904 CDS None chromosome 3038625 3038861 - Uncharacterized protein, VEG B.subtilis ortholog (NCBI ptt file) False
CAC3718 CAC3718 CDS None chromosome 3923797 3925782 - Exopolyphosphatase-like domain and PAS domain containing protein, YYBT B.subtilis ortholog (NCBI ptt file) False
CAC3719 CAC3719 CDS None chromosome 3925782 3926783 - Uncharacterized predicted membrane protein, YYBS B.subtilis homolog (NCBI ptt file) False
CAC3720 CAC3720 CDS None chromosome 3926805 3927122 - Hypothetical protein (NCBI ptt file) 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 298

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.