Organism : Clostridium acetobutylicum | Module List:
Module 259 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 259

There are 13 regulatory influences for Module 259

Regulator Table (13)
Regulator Name Type
CAC3611 tf
CAC0201 tf
CAC0360 tf
CAC2605 tf
CAC1340 tf
CAC3166 tf
CAC3687 tf
CAC3142 tf
CAC2690 tf
CAC2473 tf
CAC2608 tf
CAC0821 tf
CAC3509 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
7170 7.20e+03 GaCcGGC
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7171 6.50e+01 aGaAagaGAGg
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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 259 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 7.97e-03 1.39e-02 8/26
Transcription cog subcategory 1.28e-03 2.47e-03 6/26
Replication, recombination and repair cog subcategory 1.26e-02 2.13e-02 3/26
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 259

There are 26 genes in Module 259

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0201 CAC0201 CDS None chromosome 225955 226539 - Transcriptional regulators, AcrR family (NCBI ptt file) True
CAC0238 CAC0238 CDS None chromosome 269138 270202 + ABC transporter, permease component (NCBI ptt file) False
CAC0291 CAC0291 CDS None chromosome 346424 348214 + FUSION: methionine sintase I (cobalamin dependent) and 5,10 methylenetetrahydrofolate reductase (NCBI ptt file) False
CAC0360 CAC0360 CDS None chromosome 419727 420713 + Transcriptional regulator, LacI family (HTH lacI domain), B.subtilis degA ortholog (NCBI ptt file) True
CAC0389 CAC0389 CDS None chromosome 453595 453753 + Hypothetical protein (NCBI ptt file) False
CAC0421 CAC0421 CDS None chromosome 487214 487762 - Uncharacterized membrane protein (NCBI ptt file) False
CAC0487 CAC0487 CDS None chromosome 561992 562240 - Uncharacterized protein, ortholog of Thermotoga maritima (4981823) (NCBI ptt file) False
CAC1273 CAC1273 CDS None chromosome 1416308 1417339 + Uncharacterized protein, YQEN B.subtilis homolog (NCBI ptt file) False
CAC1340 araR CDS None chromosome 1478746 1479834 - Transcriptional regulator of the LacI family (NCBI ptt file) True
CAC1490 CAC1490 CDS None chromosome 1637095 1637268 + Hypothetical protein (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
CAC1582 CAC1582 CDS None chromosome 1725616 1726974 + Membrane associated histidine kinase-like ATPase (NCBI ptt file) False
CAC1619 CAC1619 CDS None chromosome 1759563 1759898 + Hypothetical protein (NCBI ptt file) False
CAC1677 CAC1677 CDS None chromosome 1825727 1826752 + Predicted permease (NCBI ptt file) False
CAC2429 CAC2429 CDS None chromosome 2544807 2545685 + Predicted membrane protein (NCBI ptt file) False
CAC2710 etfB CDS None chromosome 2833715 2834494 - Electron transfer flavoprotein beta-subunit (NCBI ptt file) False
CAC2778 CAC2778 CDS None chromosome 2910545 2910709 + Rubredoxin (NCBI ptt file) False
CAC2779 CAC2779 CDS None chromosome 2910825 2911022 + Hypothetical protein (NCBI ptt file) False
CAC2780 CAC2780 CDS None chromosome 2911042 2911338 + Spore coat protein, cotF related (NCBI ptt file) False
CAC2996 CAC2996 CDS None chromosome 3133673 3136831 - Superfamily II DNA/RNA helicase, SNF2 family (NCBI ptt file) False
CAC3529 CAC3529 CDS None chromosome 3725143 3725592 - Hypothetical protein (NCBI ptt file) False
CAC3530 CAC3530 CDS None chromosome 3725694 3725948 - Hypothetical protein (NCBI ptt file) False
CAC3546 CAC3546 CDS None chromosome 3741504 3743537 + Highly conserved protein containing a domain related to cellulase catalitic domain and a thioredoxin domain (NCBI ptt file) False
CAC3591 CAC3591 CDS None chromosome 3794062 3794808 - Acyl-ACP thioesterase (NCBI ptt file) False
CAC3601 CAC3601 CDS None chromosome 3802864 3803472 + Nudix (MutT) family hydrolase (NCBI ptt file) False
CAC3687 CAC3687 CDS None chromosome 3891923 3892513 + Transcriptional regulator, AcrR family (NCBI ptt file) True

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 259

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.