Organism : Clostridium acetobutylicum | Module List:
Module 20 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 20

There are 9 regulatory influences for Module 20

Regulator Table (9)
Regulator Name Type
CAC3579 tf
CAC1753 tf
CAC2889 tf
CAC0708 tf
CAC0768 tf
CAC3475 tf
CAC0977 tf
CAC3216 tf
CAC0183 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
6694 3.60e-03 t.gagagGtgA
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6695 7.60e+02 AAaTACCTccaTTaC
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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 20 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 1.55e-02 2.60e-02 7/24
Metabolism cog category 6.50e-03 1.15e-02 11/24
Translation, ribosomal structure and biogenesis cog subcategory 2.11e-02 3.46e-02 3/24
Transcription cog subcategory 1.99e-02 3.28e-02 4/24
Carbohydrate transport and metabolism cog subcategory 1.37e-02 2.31e-02 4/24
Amino acid transport and metabolism cog subcategory 1.35e-02 2.27e-02 4/24
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 20

There are 24 genes in Module 20

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0113 CAC0113 CDS None chromosome 124089 124850 + Transcriptional regulator of sugar metabolism (NCBI ptt file) True
CAC0114 CAC0114 CDS None chromosome 124880 125407 + Predicted membrane protein (NCBI ptt file) False
CAC0116 CAC0116 CDS None chromosome 125985 127874 + Carbone-monoxide dehydrogenase, beta chain (NCBI ptt file) False
CAC0433 CAC0433 CDS None chromosome 500877 502202 - Methyl-accepting chemotaxis protein (NCBI ptt file) False
CAC0650 CAC0650 CDS None chromosome 756294 756836 - Adenilate cyclase, class2 (thermophilic) (NCBI ptt file) False
CAC0701 CAC0701 CDS None chromosome 809917 810756 + Uncharacterised protein, DegV family (NCBI ptt file) False
CAC0708 CAC0708 CDS None chromosome 820041 821075 + Putative transcriptional regulator (NCBI ptt file) True
CAC0709 gapC CDS None chromosome 821221 822225 + Glyceraldehyde 3-phosphate dehydrogenase, gene gapC (NCBI ptt file) False
CAC0712 pgm CDS None chromosome 824683 826215 + 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gene (NCBI ptt file) False
CAC0990 gltX CDS None chromosome 1137161 1138618 - Glutamyl-tRNA synthetase (NCBI ptt file) False
CAC1693 ftsZ CDS None chromosome 1844677 1845798 + Cell division GTPase FtsZ (NCBI ptt file) False
CAC2095 CAC2095 CDS None chromosome 2192448 2193518 - Aminopeptidase P AMPP/PEPQ family enzyme, YQHT B.subtilis ortholog (NCBI ptt file) False
CAC2227 CAC2227 CDS None chromosome 2317702 2318343 - Phosphoserine phosphatase family enzyme (NCBI ptt file) False
CAC2264 glyA CDS None chromosome 2368162 2369397 - Glycine hydroxymethyltransferase (NCBI ptt file) False
CAC2332 spsJ CDS None chromosome 2439460 2440515 - DTDP-D-glucose 4,6-dehydratase (NCBI ptt file) False
CAC2633 CAC2633 CDS None chromosome 2741747 2742811 - Uncharaterized conserved protein, YOME B.subtilis ortholog (NCBI ptt file) False
CAC2771 CAC2771 CDS None chromosome 2901999 2902952 - Amino acid transporter (NCBI ptt file) False
CAC2779 CAC2779 CDS None chromosome 2910825 2911022 + Hypothetical protein (NCBI ptt file) False
CAC2780 CAC2780 CDS None chromosome 2911042 2911338 + Spore coat protein, cotF related (NCBI ptt file) False
CAC2889 rho CDS None chromosome 3019655 3021106 - Transcription termination factor rho (NCBI ptt file) True
CAC3097 rpsI CDS None chromosome 3250188 3250580 - Ribosomal protein S9 (NCBI ptt file) False
CAC3103 rplQ CDS None chromosome 3254512 3254856 - Ribosomal protein L17 (NCBI ptt file) False
CAC3578 fabH CDS None chromosome 3777415 3778392 - 3-oxoacyl-[acyl-carrier-protein] synthase III (NCBI ptt file) False
CAC3579 CAC3579 CDS None chromosome 3778397 3778861 - Transcriptional regulator, MarR/EmrR family (NCBI ptt file) True

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 20

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.