Organism : Clostridium acetobutylicum | Module List:
Module 185 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 185

There are 12 regulatory influences for Module 185

Regulator Table (12)
Regulator Name Type
CAC3509 tf
CAC0197 tf
CAC3481 tf
CAC1046 tf
CAC3349 tf
CAC0465 tf
CAC3687 tf
CAC0745 tf
CAC2473 tf
CAC3525 tf
CAC1800 tf
CAC0860 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
7022 7.10e+03 CAGGCC
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7023 7.20e+01 gGAtTaTAagggggaGgcgT
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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 185 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 4.29e-03 7.79e-03 5/24
Signal transduction mechanisms cog subcategory 1.36e-03 2.62e-03 5/24
Function unknown cog subcategory 2.89e-02 4.63e-02 4/24
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 185

There are 24 genes in Module 185

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0055 CAC0055 CDS None chromosome 63793 64383 + Uncharacterized predicted metal-binding protein, ortholog of Streptomyces (2808777) (NCBI ptt file) False
CAC0160 CAC0160 CDS None chromosome 182984 183433 + Predicted acetyltransferase (NCBI ptt file) False
CAC0239 CAC0239 CDS None chromosome 270213 271319 + Histidine kinase-like ATPase (NCBI ptt file) False
CAC0417 CAC0417 CDS None chromosome 483779 484117 + Similar to arsenate reductase (NCBI ptt file) False
CAC0420 CAC0420 CDS None chromosome 486326 487156 + Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) False
CAC0541 CAC0541 CDS None chromosome 629931 630677 + SAM-dependent methyltransferase (NCBI ptt file) False
CAC0597 gerKB CDS None chromosome 689267 690361 + Spore germination protein, gerKB (NCBI ptt file) False
CAC0747 CAC0747 CDS None chromosome 869373 870773 + Secreted protein containing uncharacterized conserved protein of ErfK family (NCBI ptt file) False
CAC0851 CAC0851 CDS None chromosome 978853 979620 + Ortholog ygiD E.coli (NCBI ptt file) False
CAC0860 CAC0860 CDS None chromosome 990196 990891 + Two-component response regulator (NCBI ptt file) True
CAC1040 CAC1040 CDS None chromosome 1190120 1191283 + Predicted amidohydrolases (NCBI ptt file) False
CAC1083 CAC1083 CDS None chromosome 1249908 1250546 + Predicted membrane-associated metal-binding protein (NCBI ptt file) False
CAC1490 CAC1490 CDS None chromosome 1637095 1637268 + Hypothetical protein (NCBI ptt file) False
CAC1491 CAC1491 CDS None chromosome 1637268 1637831 + Predicted ATPase (NCBI ptt file) False
CAC1557 CAC1557 CDS None chromosome 1701139 1701714 + Predicted acetyltransferase (NCBI ptt file) False
CAC1581 CAC1581 CDS None chromosome 1724906 1725610 + Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) False
CAC1670 CAC1670 CDS None chromosome 1814010 1814771 + Response regulator (CheY-like receiver domain and DNA-binding HTH domain) (NCBI ptt file) True
CAC1970 CAC1970 CDS None chromosome 2086719 2086940 - Hypothetical protein (NCBI ptt file) False
CAC2546 CAC2546 CDS None chromosome 2653807 2654502 - Transcriptional regulator, FadR family (NCBI ptt file) True
CAC2759 CAC2759 CDS None chromosome 2891279 2891965 + Response regulator (CheY receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) False
CAC3321 CAC3321 CDS None chromosome 3494331 3494807 + Uncharacterized protein homolog of yveG B.subtilis (NCBI ptt file) False
CAC3435 CAC3435 CDS None chromosome 3623967 3624434 - Hypothetical protein (NCBI ptt file) False
CAC3581 CAC3581 CDS None chromosome 3780202 3780807 - HAD superfamily hydrolase (NCBI ptt file) False
CAC3656 CAC3656 CDS None chromosome 3858433 3858699 - Uncharacterized conserved protein, yaiN/yohL 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 185

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.