Organism : Clostridium acetobutylicum | Module List:
Module 279 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 279

There are 9 regulatory influences for Module 279

Regulator Table (9)
Regulator Name Type
CAC2616 tf
CAC1430 tf
CAC0859 tf
CAC2794 tf
CAC0876 tf
CAC1689 tf
CAC1509 tf
CAC2859 tf
CAC3729 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
7210 2.20e-05 .gtGgAGGtAA
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7211 1.70e+04 gGAgAggGtTT
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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 279 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 2.58e-02 4.17e-02 8/27
Function unknown cog subcategory 1.25e-02 2.12e-02 5/27
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 279

There are 27 genes in Module 279

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0011 CAC0011 CDS None chromosome 18653 19513 + Uncharacterized conserved of ErfK family (NCBI ptt file) False
CAC0205 CAC0205 CDS None chromosome 229452 231410 - Predicted phosphohydrolases, Icc family (NCBI ptt file) False
CAC0262 CAC0262 CDS None chromosome 294652 295164 + Tryptophan-rich possible sensory protein, TSPO homolog (NCBI ptt file) False
CAC0354 CAC0354 CDS None chromosome 411418 413052 - Uncharacterized membrane protein (NCBI ptt file) False
CAC0604 CAC0604 CDS None chromosome 699769 700434 + Acyl carrier protein phosphodiesterase (NCBI ptt file) False
CAC0793 CAC0793 CDS None chromosome 915054 916100 + Uncharacterized conserved protein of probably eukaryotic origin (NCBI ptt file) False
CAC1520 CAC1520 CDS None chromosome 1663597 1663962 - Hypothetical protein (NCBI ptt file) False
CAC1657 CAC1657 CDS None chromosome 1802337 1802987 + Uncharacterized conserved protein, yisX B.subtilis ortholog (NCBI ptt file) False
CAC1662 CAC1662 CDS None chromosome 1805610 1806107 + Hypothetical protein (NCBI ptt file) False
CAC1985 CAC1985 CDS None chromosome 2098803 2099159 - Hypothetical protein (NCBI ptt file) False
CAC2034 CAC2034 CDS None chromosome 2142219 2142407 - Hypothetical protein (NCBI ptt file) False
CAC2089 CAC2089 CDS None chromosome 2188430 2189578 - Stage III sporulation protein AE, SpoIIIAE (NCBI ptt file) False
CAC2345 CAC2345 CDS None chromosome 2456106 2456912 - Glycosyltransferase (NCBI ptt file) False
CAC2352 CAC2352 CDS None chromosome 2462276 2462557 - Hypothetical protein (NCBI ptt file) False
CAC2353 CAC2353 CDS None chromosome 2462571 2463581 - Hypothetical protein (NCBI ptt file) False
CAC2354 CAC2354 CDS None chromosome 2463605 2464744 - Nifs family aminotransferase (NCBI ptt file) False
CAC2363 CAC2363 CDS None chromosome 2473874 2474749 - Uncharacterized protein, YtxC B.subtilis homolog (NCBI ptt file) False
CAC2412 CAC2412 CDS None chromosome 2529722 2530684 - Hypothetical protein (NCBI ptt file) False
CAC2459 CAC2459 CDS None chromosome 2574482 2576158 - 2-oxoacid:ferredoxin oxidoreductase, alpha subunit (NCBI ptt file) False
CAC2569 CAC2569 CDS None chromosome 2671556 2671951 + NimC/NimA family protein (NCBI ptt file) False
CAC2679 CAC2679 CDS None chromosome 2798521 2800683 + Pullulanase (NCBI ptt file) False
CAC2843 CAC2843 CDS None chromosome 2974283 2975632 + Protein containing aminopeptidase domain (iap family) (NCBI ptt file) False
CAC2863 CAC2863 CDS None chromosome 2997945 2998652 - Predicted membrane protein (NCBI ptt file) False
CAC2941 CAC2941 CDS None chromosome 3072708 3073514 - HAD superfamily hydrolase (NCBI ptt file) False
CAC2945 CAC2945 CDS None chromosome 3077796 3078770 - Possible phosphoglycerate dehydrogenase (NCBI ptt file) False
CAC3031 hisC CDS None chromosome 3172870 3173928 - Histidinol-phosphate aminotransferase (NCBI ptt file) False
CAC3204 CAC3204 CDS None chromosome 3350269 3351654 - Cell cycle protein MesJ ortholog, ATPase of the PP-loop superamily (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 279

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.