Organism : Clostridium acetobutylicum | Module List:
Module 207 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 207

There are 5 regulatory influences for Module 207

Regulator Table (5)
Regulator Name Type
CAC0093 tf
CAC0144 tf
CAC3466 tf
CAC3509 tf
CAC0197 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
7066 4.30e-11 gAGGtGat
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7067 7.10e+02 AGcaGtggCc
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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 207 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.42e-02 2.38e-02 9/27
Defense mechanisms cog subcategory 3.14e-03 5.79e-03 3/27
Cell motility cog subcategory 6.69e-03 1.18e-02 3/27
Methyl-accepting chemotaxis protein cog 5.60e-05 1.62e-04 3/27
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 207

There are 27 genes in Module 207

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0168 CAC0168 CDS None chromosome 191046 191867 + T-RNA-processing ribonuclease BN (NCBI ptt file) False
CAC0204 srta CDS None chromosome 228731 229315 - Sortase (surface protein transpeptidase), YHCS B.subtilis ortholog (NCBI ptt file) False
CAC0222 exoA CDS None chromosome 246602 247354 + Exodeoxyribonuclease (exoA) (NCBI ptt file) False
CAC0250 CAC0250 CDS None chromosome 279643 281709 + Methyl-accepting chemotaxis protein (NCBI ptt file) False
CAC0314 CAC0314 CDS None chromosome 368391 368984 + Uncharacterized protein homolog YKRK B. subtilis (NCBI ptt file) False
CAC0345 CAC0345 CDS None chromosome 403554 403760 + Hypothetical protein (NCBI ptt file) False
CAC0357 CAC0357 CDS None chromosome 415725 417266 - Permease of the Na:galactoside symporter family (NCBI ptt file) False
CAC0358 CAC0358 CDS None chromosome 417308 418108 - Predicted xylanase/chitin deacetylase (NCBI ptt file) False
CAC0431 CAC0431 CDS None chromosome 498497 499372 - Hypothetical protein, YitT family (NCBI ptt file) False
CAC0440 CAC0440 CDS None chromosome 507499 507936 - Homolog of osmotically induced OSMY protein of E.coli (NCBI ptt file) False
CAC0463 CAC0463 CDS None chromosome 534787 535833 - Serine protease Do (heat-shock protein) (NCBI ptt file) False
CAC0543 CAC0543 CDS None chromosome 632838 634577 + Methyl-accepting chemotaxis protein (NCBI ptt file) False
CAC0628 CAC0628 CDS None chromosome 730162 731415 + Putative Mn transporter, NRAMR family (NCBI ptt file) False
CAC0805 CAC0805 CDS None chromosome 930520 932526 + Methyl-accepting chemotaxis protein (NCBI ptt file) False
CAC0833 CAC0833 CDS None chromosome 964104 964841 + ABC-type multidrug transport system (daunorubicin resistance), ATPase component (NCBI ptt file) False
CAC0835 CAC0835 CDS None chromosome 965598 966656 + Predicted integral membrane protein (NCBI ptt file) False
CAC0886 CAC0886 CDS None chromosome 1015110 1016195 + Hypothetical protein (NCBI ptt file) False
CAC1422 CAC1422 CDS None chromosome 1566594 1567880 + Uncharacterized CBS domain-containing protein, YUGS B.subtilis ortholog (NCBI ptt file) False
CAC2057 CAC2057 CDS None chromosome 2161783 2162838 - D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) False
CAC2540 CAC2540 CDS None chromosome 2648662 2649573 - Co/Zn/Cd efflux system component (NCBI ptt file) False
CAC2814 CAC2814 CDS None chromosome 2944093 2944548 - Predicted membrane protein (NCBI ptt file) False
CAC2949 CAC2949 CDS None chromosome 3083542 3084459 + Predicted permease (NCBI ptt file) False
CAC3347 CAC3347 CDS None chromosome 3520108 3521583 - Amino acid transporter, permease (NCBI ptt file) False
CAC3468 uvrC CDS None chromosome 3666507 3667628 - Excinuclease ABC, subunit C (uvrC) (NCBI ptt file) False
CAC3478 CAC3478 CDS None chromosome 3679350 3679955 + Predicted membrane protein (NCBI ptt file) False
CAC3519 CAC3519 CDS None chromosome 3717187 3717840 - Predicted membrane protein, possible permease (NCBI ptt file) False
CAC3520 CAC3520 CDS None chromosome 3717860 3718804 - ABC-type transport system, ATPase component (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 207

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.