Organism : Clostridium acetobutylicum | Module List:
Module 315 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 315

There are 20 regulatory influences for Module 315

Regulator Table (20)
Regulator Name Type
CAC1799 tf
CAC3192 tf
CAC1753 tf
CAC2773 tf
CAC2084 tf
CAC2473 tf
CAC1467 tf
CAC3418 tf
CAC2259 tf
CAC0856 tf
CAC0113 tf
CAC2950 tf
CAC0197 tf
CAC2143 tf
CAC1689 tf
CAC2546 tf
CAC0382 tf
CAC3166 tf
CAC1696 tf
CAC3502 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
7282 4.10e-01 gGAGttGg
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7283 7.50e+01 ctGtAGcaAg
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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 315 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein synthesis tigr mainrole 8.04e-03 1.08e-02 3/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Replication, recombination and repair cog subcategory 9.46e-03 1.63e-02 3/24
Cell wall/membrane/envelope biogenesis cog subcategory 5.21e-03 9.34e-03 4/24
General function prediction only cog subcategory 4.60e-03 8.31e-03 6/24
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 315

There are 24 genes in Module 315

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0300 CAC0300 CDS None chromosome 355339 356283 + DNA-polymerase III, gamma subunit (NCBI ptt file) False
CAC0491 CAC0491 CDS None chromosome 565084 565719 + Uncharacterized probably secreted protein, homolog of YDCC B.subtilis (NCBI ptt file) False
CAC1026 CAC1026 CDS None chromosome 1176126 1178417 + Superfamily I DNA helicase (NCBI ptt file) False
CAC1243 mreC CDS None chromosome 1383068 1383919 + Shape-determining protein mreC (NCBI ptt file) False
CAC1305 CAC1305 CDS None chromosome 1449041 1450537 + Uncharacterized protein similar to a protein from Cylindrotheca fusiformis plasmid (GI:99322) (NCBI ptt file) False
CAC1403 CAC1403 CDS None chromosome 1546703 1547599 + Zn-dependent hydrolase, glyoxylase II family (NCBI ptt file) False
CAC1468 CAC1468 CDS None chromosome 1617414 1617842 + Predicted acetyltransferase (NCBI ptt file) False
CAC1684 CAC1684 CDS None chromosome 1833236 1835053 + TYPA/BIPA type GTPase (NCBI ptt file) False
CAC1685 CAC1685 CDS None chromosome 1835074 1836093 + Uncharacterized protein from YceG family (NCBI ptt file) False
CAC1686 CAC1686 CDS None chromosome 1836109 1836759 + S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) False
CAC1687 CAC1687 CDS None chromosome 1836752 1837972 + Collagenase family protease (NCBI ptt file) False
CAC1689 sigK CDS None chromosome 1839816 1840520 + DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) True
CAC1725 CAC1725 CDS None chromosome 1873652 1874977 + Predicted rRNA methylase, SUN family (NCBI ptt file) False
CAC1729 CAC1729 CDS None chromosome 1878756 1879622 + Predicted GTPase (YLOQ B.subtilis ortholog) (NCBI ptt file) False
CAC1730 CAC1730 CDS None chromosome 1879619 1880269 + Pentose-5-phosphate-3-epimerase, YLOR B.subtilis ortholog (NCBI ptt file) False
CAC1790 frr CDS None chromosome 1939847 1940404 + Ribosome recycling factor (NCBI ptt file) False
CAC1823 CAC1823 CDS None chromosome 1973730 1974035 + Uncharacterized conserved protein (NCBI ptt file) False
CAC1824 clpA CDS None chromosome 1974039 1976291 + ATP-dependent Clp proteinase (NCBI ptt file) False
CAC1829 CAC1829 CDS None chromosome 1979944 1981308 + Predicted inactivated Zn-dependent peptidase, PMBA ortholog (NCBI ptt file) False
CAC2232 recJ CDS None chromosome 2324966 2326729 - SsDNA Exonuclease, RecJ (NCBI ptt file) False
CAC2673 CAC2673 CDS None chromosome 2789552 2791561 - NAD-dependent DNA ligase (NCBI ptt file) False
CAC2874 CAC2874 CDS None chromosome 3007468 3008625 - UDP-N-acetylglucosamine 2-epimerase (NCBI ptt file) False
CAC3032 CAC3032 CDS None chromosome 3174101 3174997 - Galactose mutarotase related enzyme (NCBI ptt file) False
CAC3594 CAC3594 CDS None chromosome 3796638 3797834 - Glycosyltransferase (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 315

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.