Organism : Clostridium acetobutylicum | Module List:
Module 53 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 53

There are 13 regulatory influences for Module 53

Regulator Table (13)
Regulator Name Type
CAC0115 tf
CAC0821 tf
CAC0863 tf
CAC2471 tf
CAC1320 tf
CAC3673 tf
CAC0081 tf
CAC0627 tf
CAC3677 tf
CAC3198 tf
CAC3409 tf
CAC0949 tf
CAC0708 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
6760 4.40e-02 gtAaaAaggGGAaG.
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6761 1.30e+04 GCTGCaGc
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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 53 is enriched for following functions.

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 53

There are 29 genes in Module 53

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0081 agrA CDS None chromosome 88953 89678 + Accessory gene regulator protein A (NCBI ptt file) True
CAC0437 CAC0437 CDS None chromosome 504464 506377 + Sensory transduction histidine kinase (NCBI ptt file) False
CAC0639 CAC0639 CDS None chromosome 744438 744710 + Flagellar biosynthesis related protein (NCBI ptt file) False
CAC0716 smpB CDS None chromosome 830436 830903 + TmRNA-binding protein SmpB (NCBI ptt file) False
CAC0831 CAC0831 CDS None chromosome 962099 963199 + Sensory transduction histidine kinase (NCBI ptt file) False
CAC0910 CAC0910 CDS None chromosome 1043161 1047612 + Probably cellulosomal scaffolding protein precursor, secreted; cellulose-binding and cohesin domain (NCBI ptt file) False
CAC0912 CAC0912 CDS None chromosome 1049962 1051410 + Possible non-processive endoglucanase family 5, secreted; CelA homolog secreted; dockerin domain (NCBI ptt file) False
CAC0925 CAC0925 CDS None chromosome 1068171 1069211 + TPR-repeat-containing protein (NCBI ptt file) False
CAC1078 CAC1078 CDS None chromosome 1229863 1230933 - Predicted phosphohydrolase, Icc family (NCBI ptt file) False
CAC1169 CAC1169 CDS None chromosome 1326867 1327145 + Hypothetical protein (NCBI ptt file) False
CAC1170 xerD CDS None chromosome 1327295 1328194 + Integrase/recombinase (xerD/xerC family) (NCBI ptt file) False
CAC1228 cisA CDS None chromosome 1370501 1372135 + Site-specific DNA recombinase (NCBI ptt file) False
CAC1452 CAC1452 CDS None chromosome 1600181 1601617 + MDR-type permease (NCBI ptt file) False
CAC1555 CAC1555 CDS None chromosome 1698584 1699420 - Flagellin (NCBI ptt file) False
CAC1770 CAC1770 CDS None chromosome 1915404 1916105 + RNA polymerase sigma factor, SigK-like (NCBI ptt file) True
CAC1772 sacB1 CDS None chromosome 1916997 1918466 + Levansucrase (NCBI ptt file) False
CAC1914 CAC1914 CDS None chromosome 2051557 2051829 - Hypothetical protein (NCBI ptt file) False
CAC1994 moaB CDS None chromosome 2105694 2106284 - Molybdopterin biosynthesis enzyme, MoaB (NCBI ptt file) False
CAC2013 CAC2013 CDS None chromosome 2126238 2126906 - Hypothetical protein (NCBI ptt file) False
CAC2015 CAC2015 CDS None chromosome 2127284 2127808 - Hypothetical protein (NCBI ptt file) False
CAC2133 CAC2133 CDS None chromosome 2224376 2224804 - Uncharacterized conserved protein, YLLB B.subtilis family (NCBI ptt file) False
CAC2336 CAC2336 CDS None chromosome 2443468 2444541 - TPR repeats containing protein (NCBI ptt file) False
CAC2494 CAC2494 CDS None chromosome 2601128 2601538 - Predicted membrane protein (NCBI ptt file) False
CAC2504 CAC2504 CDS None chromosome 2612211 2612447 - Hypothetical protein (NCBI ptt file) False
CAC2706 CAC2706 CDS None chromosome 2830041 2830751 - Uncharacterized conserved membrane protein, DedA family (NCBI ptt file) False
CAC2715 CAC2715 CDS None chromosome 2839785 2839979 + Hypothetical protein (NCBI ptt file) False
CAC2727 CAC2727 CDS None chromosome 2851563 2852330 - Predicted PHP family hydrolase (NCBI ptt file) False
CAC3215 prsA CDS None chromosome 3361034 3362095 - Parvulin-like peptidyl-prolyl isomerase, PRSA B.subtilis ortholog (NCBI ptt file) False
CAC3535 CAC3535 CDS None chromosome 3729301 3732282 - Type II restriction enzyme, methylase subunit (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 53

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.