Organism : Clostridium acetobutylicum | Module List:
Module 304 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 304

There are 11 regulatory influences for Module 304

Regulator Table (11)
Regulator Name Type
CAC3647 tf
CAC2476 tf
CAC3104 tf
CAC1950 tf
CAC1426 tf
CAC1719 tf
CAC0115 tf
CAC1536 tf
CAC2966 tf
CAC0707 tf
CAC0977 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
7260 7.50e-04 gTaatTaaggAGGtg
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7261 7.30e-01 GGAaGAAgg
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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 304 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 1.23e-03 2.08e-03 3/27
ATP-proton motive force interconversion tigr sub1role 0.00e+00 0.00e+00 3/27
Protein synthesis tigr mainrole 2.28e-04 4.69e-04 5/27
Ribosomal proteins: synthesis and modification tigr sub1role 3.93e-04 7.62e-04 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 6.41e-03 1.13e-02 4/27
Energy production and conversion cog subcategory 1.13e-02 1.93e-02 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 304

There are 27 genes in Module 304

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0128 CAC0128 CDS None chromosome 139230 139490 + Hypothetical protein (NCBI ptt file) False
CAC0129 bofA CDS None chromosome 139498 139770 + BofA B.subtilis ortholog, SigmaK-factor processing regulatory protein (NCBI ptt file) False
CAC0228 CAC0228 CDS None chromosome 253559 253861 - Hypothetical protein (NCBI ptt file) False
CAC0546 CAC0546 CDS None chromosome 635596 635946 + Uncharacterized membrane protein, homolog of Methanobacterium (2621593) (NCBI ptt file) False
CAC0716 smpB CDS None chromosome 830436 830903 + TmRNA-binding protein SmpB (NCBI ptt file) False
CAC0730 CAC0730 CDS None chromosome 844892 846043 + Predicted permease (NCBI ptt file) False
CAC0771 CAC0771 CDS None chromosome 893874 894842 + Cobalamin biosynthesis protein CbiM (NCBI ptt file) False
CAC0868 CAC0868 CDS None chromosome 997544 998593 + Predicted membrane protein (NCBI ptt file) False
CAC1065 CAC1065 CDS None chromosome 1217964 1218590 + Uncharacterized protein, related stage III sporulation protein AH of Bacillus sp. (NCBI ptt file) False
CAC1274 rpsT CDS None chromosome 1417389 1417655 - Ribosomal protein S20 (NCBI ptt file) False
CAC1334 CAC1334 CDS None chromosome 1473808 1474899 + Fe-S oxidoreductase of MoeA/NarA subfamily (NCBI ptt file) False
CAC1740 CAC1740 CDS None chromosome 1887606 1888751 - Uncharcaterized membrane protein, YLBJ B.subtilis homolog (NCBI ptt file) False
CAC2110 CAC2110 CDS None chromosome 2202996 2203496 - GAF domain-containing protein (NCBI ptt file) False
CAC2299 hflX CDS None chromosome 2401972 2403753 - Predicted GTPase, HflX (NCBI ptt file) False
CAC2476 CAC2476 CDS None chromosome 2586521 2586865 - Uncharacterized protein, homolog of Spirochaeta aurantia (gi:152901) (NCBI ptt file) True
CAC2477 CAC2477 CDS None chromosome 2586897 2587856 - Hypothetical protein (NCBI ptt file) False
CAC2641 tig CDS None chromosome 2751970 2753265 - FKBP-type peptidyl-prolyl cis-transisomerase (trigger factor) (NCBI ptt file) False
CAC2864 atpC CDS None chromosome 2998857 2999258 - FoF1-type ATP synthase epsilon subunit (NCBI ptt file) False
CAC2865 atpD CDS None chromosome 2999272 3000672 - FoF1-type ATP synthase beta subunit (NCBI ptt file) False
CAC2870 atpE CDS None chromosome 3004163 3004408 - FoF1-type ATP synthase C subunit (NCBI ptt file) False
CAC2888 rpmE CDS None chromosome 3019235 3019447 + 50S ribosomal protein L31 (NCBI ptt file) False
CAC3038 ileS CDS None chromosome 3184955 3188062 - Isoleucyl-tRNA synthetase (NCBI ptt file) False
CAC3104 rpoA CDS None chromosome 3254878 3255825 - DNA-dependent RNA polymerase alpha subunit (NCBI ptt file) True
CAC3113 seqY CDS None chromosome 3259515 3260798 - Preprotein translocase subunit SecY (NCBI ptt file) False
CAC3122 rplX CDS None chromosome 3264108 3264428 - Ribosomal protein L24 (NCBI ptt file) False
CAC3647 abrB CDS None chromosome 3847785 3848030 - Transition state regulatory protein AbrB (NCBI ptt file) True
CAC3700 CAC3700 CDS None chromosome 3904309 3904788 - Hypothetical protein, CF-44 family (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 304

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.