Organism : Clostridium acetobutylicum | Module List:
Module 100 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 100

There are 12 regulatory influences for Module 100

Regulator Table (12)
Regulator Name Type
CAC1578 tf
CAC3143 tf
CAC1696 tf
CAC2254 tf
CAC3611 tf
CAC2430 tf
CAC2950 tf
CAC3466 tf
CAC0766 tf
CAC0859 tf
CAC1463 tf
CAC1689 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
6852 3.40e-01 AGGaGGTG
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6853 7.10e+03 GGAGGC
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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 100 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 7.71e-03 1.35e-02 9/25
Signal transduction mechanisms cog subcategory 9.54e-03 1.65e-02 4/25
Cell wall/membrane/envelope biogenesis cog subcategory 3.10e-02 4.94e-02 3/25
General function prediction only cog subcategory 2.29e-02 3.74e-02 5/25
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 100

There are 25 genes in Module 100

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0121 cheR CDS None chromosome 132669 133481 + Chemotaxis protein methyltransferase (cheR) (NCBI ptt file) False
CAC0355 CAC0355 CDS None chromosome 413374 414915 - Putative polygalacturonase (pectinase) (NCBI ptt file) False
CAC0456 lonA CDS None chromosome 525052 527412 - ATP-dependent protease (lonA) (NCBI ptt file) False
CAC0994 CAC0994 CDS None chromosome 1141644 1141991 - Predicted membrane protein (NCBI ptt file) False
CAC1387 CAC1387 CDS None chromosome 1528839 1530554 + Membrane associated chemotaxis sensory transducer protein (MSP domain and HAMP domain) (NCBI ptt file) False
CAC1403 CAC1403 CDS None chromosome 1546703 1547599 + Zn-dependent hydrolase, glyoxylase II family (NCBI ptt file) False
CAC1483 CAC1483 CDS None chromosome 1630694 1631020 - Predicted transcriptional regulator (NCBI ptt file) True
CAC1572 CAC1572 CDS None chromosome 1716058 1718055 + Fructose-1,6-bisphosphatase (YYDE B.subtils ortholog) (NCBI ptt file) False
CAC1701 CAC1701 CDS None chromosome 1851064 1852764 + Sensory histidine kinase (with HAMP and PAS domains) (NCBI ptt file) False
CAC2243 asnB CDS None chromosome 2338031 2339224 + N-terminal domain of asparagine synthase (NCBI ptt file) False
CAC2254 CAC2254 CDS None chromosome 2353179 2353820 + Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) True
CAC2343 CAC2343 CDS None chromosome 2454438 2454986 - LPS biosynthesis O-acetyl transferase (NCBI ptt file) False
CAC2345 CAC2345 CDS None chromosome 2456106 2456912 - Glycosyltransferase (NCBI ptt file) False
CAC2346 CAC2346 CDS None chromosome 2456938 2457759 - Glycosyltransferase (NCBI ptt file) False
CAC2349 CAC2349 CDS None chromosome 2459470 2460255 - Hypothetical protein (NCBI ptt file) False
CAC2350 CAC2350 CDS None chromosome 2460248 2461342 - Sugar transaminase, involved in dTDP-4-amino-4,6-dideoxyglucose biosynthesis (NCBI ptt file) False
CAC2351 CAC2351 CDS None chromosome 2461370 2462128 - Glycosyltransferase (NCBI ptt file) False
CAC2437 CAC2437 CDS None chromosome 2554635 2555234 + Uncharacterized conserved protein (NCBI ptt file) False
CAC2844 galT CDS None chromosome 2975675 2976619 - Galactose-1-phosphate uridylyltransferase (NCBI ptt file) False
CAC2846 secA CDS None chromosome 2977874 2980393 - Preprotein translocase subunit SecA (ATPase, RNA helicase) (NCBI ptt file) False
CAC3003 thyA CDS None chromosome 3140970 3141761 + Thymidylate synthase (NCBI ptt file) False
CAC3299 bdhA CDS None chromosome 3464035 3465204 - NADH-dependent butanol dehydrogenase A (BDH I) (NCBI ptt file) False
CAC3586 cinA CDS None chromosome 3785633 3786868 - Competence-damage inducible protein, CINA (NCBI ptt file) False
CAC3660 CAC3660 CDS None chromosome 3862248 3863183 + Uncharacterized protein, homolog of Desulfovibrio gigas (gi:6978031) (NCBI ptt file) False
CAC3734 thdF CDS None chromosome 3937124 3938503 - Predicted GTPase, ThdF 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 100

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.