Organism : Clostridium acetobutylicum | Module List:
Module 312 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 312

There are 11 regulatory influences for Module 312

Regulator Table (11)
Regulator Name Type
CAC3345 tf
CAC2939 tf
CAC3166 tf
CAC3488 tf
CAC1032 tf
CAC0201 tf
CAC2254 tf
CAC3466 tf
CAC1578 tf
CAC0933 tf
CAC0859 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
7276 1.40e-02 aaGGaGG
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7277 2.50e+03 tAaaag.g.GagaAA
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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 312 is enriched for following functions.

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 312

There are 34 genes in Module 312

Gene Member Table (34)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0009 CAC0009 CDS None chromosome 15285 15800 + Uncharacterized conserved protein, ortholog of YRXA B.subtilis (NCBI ptt file) False
CAC0010 CAC0010 CDS None chromosome 15826 18546 + Uncharacterized conserved protein, possible metal-binding (NCBI ptt file) False
CAC0043 CAC0043 CDS None chromosome 56937 57458 + Hypothetical protein, CF-3 family (NCBI ptt file) False
CAC0044 CAC0044 CDS None chromosome 57468 57743 + Predicted membrane protein (NCBI ptt file) False
CAC0090 CAC0090 CDS None chromosome 97839 98720 + Xylanase/chitin deacetylase, NodB family (NCBI ptt file) False
CAC0354 CAC0354 CDS None chromosome 411418 413052 - Uncharacterized membrane protein (NCBI ptt file) False
CAC0618 CAC0618 CDS None chromosome 719161 719955 - Uncharacterised permease, similar to ABC transporter (permease) (NCBI ptt file) False
CAC0726 CAC0726 CDS None chromosome 840170 840640 - Ribose 5-phosphate isomerase RpiB (NCBI ptt file) False
CAC0915 CAC0915 CDS None chromosome 1054263 1056083 + Endoglucanase A precursor (endo-1,4-beta-glucanase) (cellulase A), secreted; dockerin domain (NCBI ptt file) False
CAC1271 CAC1271 CDS None chromosome 1414563 1415417 + ComC competence related protein (NCBI ptt file) False
CAC1277 CAC1277 CDS None chromosome 1420001 1420495 + Predicted membrane protein (NCBI ptt file) False
CAC1635 CAC1635 CDS None chromosome 1776707 1777555 - Predicted nucleic acid binding protein, containing 2 S1 domains, YITL B.subtilis ortholog (NCBI ptt file) False
CAC1829 CAC1829 CDS None chromosome 1979944 1981308 + Predicted inactivated Zn-dependent peptidase, PMBA ortholog (NCBI ptt file) False
CAC1860 CAC1860 CDS None chromosome 2011191 2012177 + Predicted flavodoxin oxidoreductase (NCBI ptt file) False
CAC1956 CAC1956 CDS None chromosome 2072361 2073956 + Site-specific recombinases, DNA invertase Pin homolog (NCBI ptt file) False
CAC2033 CAC2033 CDS None chromosome 2141608 2142201 - Hypothetical protein (NCBI ptt file) False
CAC2037 CAC2037 CDS None chromosome 2143858 2144517 - Hypothetical protein, CF-39 family (NCBI ptt file) False
CAC2038 CAC2038 CDS None chromosome 2144564 2144914 - Hypothetical protein, CF-23 family (NCBI ptt file) False
CAC2096 CAC2096 CDS None chromosome 2193697 2194086 - Hypothetical protein (NCBI ptt file) False
CAC2098 CAC2098 CDS None chromosome 2194543 2195271 - Hypothetical protein (NCBI ptt file) False
CAC2102 CAC2102 CDS None chromosome 2196303 2196776 - Prepilin peptidase (NCBI ptt file) False
CAC2251 CAC2251 CDS None chromosome 2345430 2347601 - Uncharacterized conserved membrane protein, affecting LPS biosynthesis (NCBI ptt file) False
CAC2348 CAC2348 CDS None chromosome 2458666 2459457 - Glycosyltransferase (NCBI ptt file) False
CAC2431 CAC2431 CDS None chromosome 2546553 2548457 - Alkaline phosphatase superfamily enzyme (NCBI ptt file) False
CAC2434 CAC2434 CDS None chromosome 2551088 2552566 - Membrane associatehistidine kinase with HAMP domain (NCBI ptt file) False
CAC2491 CAC2491 CDS None chromosome 2598885 2599352 + Predicted acetyltransferase (NCBI ptt file) False
CAC2719 CAC2719 CDS None chromosome 2843331 2844647 - Ethanolamin permease (NCBI ptt file) False
CAC2831 CAC2831 CDS None chromosome 2961113 2961808 + Conserved membrane protein, YccA family (NCBI ptt file) False
CAC2908 CAC2908 CDS None chromosome 3043298 3044332 - Spore coat protein cotS related (NCBI ptt file) False
CAC2910 CAC2910 CDS None chromosome 3045114 3046121 - Spore coat protein cotS related (NCBI ptt file) False
CAC3222 gcaD CDS None chromosome 3371311 3372681 - UDP-N-acetylglucosamine pyrophosphorylase (NCBI ptt file) False
CAC3236 CAC3236 CDS None chromosome 3385423 3386361 - Possible transcriptional regulator from YAEG/LRPR family (NCBI ptt file) True
CAC3237 msmX CDS None chromosome 3386375 3387484 - Multiple sugar-binding ABC-transporter, MSMX ATP-binding protein (NCBI ptt file) False
CAC3491 CAC3491 CDS None chromosome 3688054 3688491 + Protein, related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase 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 312

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.