Organism : Clostridium acetobutylicum | Module List:
Module 180 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 180

There are 5 regulatory influences for Module 180

Regulator Table (5)
Regulator Name Type
CAC1946 tf
CAC1900 tf
CAC1945 tf
CAC2966 tf
CAC1867 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
7012 1.70e+02 GGGcgcT
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7013 3.10e+03 gA.atatg.cg.A.Ac.T
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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 180 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Mobile and extrachromosomal element functions tigr mainrole 0.00e+00 0.00e+00 8/29
Prophage functions tigr sub1role 0.00e+00 0.00e+00 8/29

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 180

There are 29 genes in Module 180

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC1875 CAC1875 CDS None chromosome 2022095 2022658 - Hypothetical protein, CF-36 family (NCBI ptt file) False
CAC1876 lyc CDS None chromosome 2022678 2023733 - N-acetylmuramidase, autolytic enzyme, family 25 of glycosyl hydrolases ; peptodoglycan-binding domain (NCBI ptt file) False
CAC1877 CAC1877 CDS None chromosome 2023751 2024008 - Hypothetical protein, CF-8 family (NCBI ptt file) False
CAC1878 CAC1878 CDS None chromosome 2024020 2024286 - Hypothetical protein (NCBI ptt file) False
CAC1879 CAC1879 CDS None chromosome 2024316 2028527 - Uncharacterized, phage-related protein (NCBI ptt file) False
CAC1880 CAC1880 CDS None chromosome 2028559 2028933 - Hypothetical protein, CF-35 family (NCBI ptt file) False
CAC1882 CAC1882 CDS None chromosome 2029205 2030413 - Hypothetical protein (NCBI ptt file) False
CAC1883 CAC1883 CDS None chromosome 2030415 2035874 - Uncharacterized phage related protein (NCBI ptt file) False
CAC1884 CAC1884 CDS None chromosome 2035908 2036063 - Hypothetical protein (NCBI ptt file) False
CAC1885 CAC1885 CDS None chromosome 2036090 2036419 - Hypothetical protein (NCBI ptt file) False
CAC1886 CAC1886 CDS None chromosome 2036473 2037393 - Uncharacterized phage related protein (NCBI ptt file) False
CAC1887 CAC1887 CDS None chromosome 2037438 2037761 - Hypothetical protein (NCBI ptt file) False
CAC1888 CAC1888 CDS None chromosome 2037758 2038189 - Uncharacterized phage related protein (NCBI ptt file) False
CAC1889 CAC1889 CDS None chromosome 2038190 2038537 - Uncharacterized phage related protein (NCBI ptt file) False
CAC1890 CAC1890 CDS None chromosome 2038500 2038817 - Phage related protein, possible DNA packing (NCBI ptt file) False
CAC1892 CAC1892 CDS None chromosome 2039105 2040295 - Hypothetical protein (NCBI ptt file) False
CAC1893 CAC1893 CDS None chromosome 2040297 2041067 - ClpP family serine protease, possible phage related (NCBI ptt file) False
CAC1894 CAC1894 CDS None chromosome 2041030 2042289 - Phage-related, head portal protein (NCBI ptt file) False
CAC1896 CAC1896 CDS None chromosome 2044051 2044506 - Phage terminase-like protein, small subunit (NCBI ptt file) False
CAC1897 CAC1897 CDS None chromosome 2044682 2044993 - Phage-related, Zn finger domain containing protein (NCBI ptt file) False
CAC1898 CAC1898 CDS None chromosome 2045000 2045263 - Hypothetical protein (NCBI ptt file) False
CAC1899 CAC1899 CDS None chromosome 2045358 2045735 - Hypothetical protein (NCBI ptt file) False
CAC1902 CAC1902 CDS None chromosome 2046283 2046480 - Hypothetical protein (NCBI ptt file) False
CAC1903 CAC1903 CDS None chromosome 2046440 2046658 - Hypothetical protein (NCBI ptt file) False
CAC1904 CAC1904 CDS None chromosome 2046962 2047156 - Hypothetical protein (NCBI ptt file) False
CAC1906 CAC1906 CDS None chromosome 2047861 2048061 - Hypothetical protein (NCBI ptt file) False
CAC1907 CAC1907 CDS None chromosome 2048076 2048240 - Hypothetical protein (NCBI ptt file) False
CAC1908 CAC1908 CDS None chromosome 2048246 2048443 - Predicted membrane protein (NCBI ptt file) False
CAC1913 CAC1913 CDS None chromosome 2051108 2051326 - Zn-finger containing 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 180

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.