Organism : Clostridium acetobutylicum | Module List:
Module 44 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 44

There are 10 regulatory influences for Module 44

Regulator Table (10)
Regulator Name Type
CAC0299 tf
CAC2430 tf
CAC0144 tf
CAC1869 tf
CAC1536 tf
CAC0763 tf
CAC2568 tf
CAC0832 tf
CAC1569 tf
CAC2476 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
6742 7.70e-03 aAAGGaG
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6743 5.30e+03 CA.g.caACaGgaAGCT
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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 44 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein fate tigr mainrole 9.93e-04 1.73e-03 3/30
Protein and peptide secretion and trafficking tigr sub1role 2.90e-05 7.60e-05 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 6.49e-03 1.15e-02 10/30
Signal transduction mechanisms cog subcategory 2.06e-02 3.38e-02 4/30
Function unknown cog subcategory 5.37e-03 9.61e-03 6/30
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 44

There are 30 genes in Module 44

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0038 CAC0038 CDS None chromosome 49650 49895 + Hypothetical protein (NCBI ptt file) False
CAC0070 CAC0070 CDS None chromosome 79854 80822 - Hypothetical protein (NCBI ptt file) False
CAC0188 nagA CDS None chromosome 213176 214321 - N-acetylglucosamine-6-phosphate deacetylase (gene nagA) (NCBI ptt file) False
CAC0441 CAC0441 CDS None chromosome 508089 508868 + Uncharacterized conserved membrane protein of SANA family (NCBI ptt file) False
CAC0509 CAC0509 CDS None chromosome 585799 586533 + PHP family protein (NCBI ptt file) False
CAC0764 CAC0764 CDS None chromosome 886021 887256 + NADPH-dependent glutamate synthase beta chain (NCBI ptt file) False
CAC0946 CAC0946 CDS None chromosome 1085697 1086659 + ComE-like protein, Metallo beta-lactamase superfamily hydrolase, secreted (NCBI ptt file) False
CAC1552 CAC1552 CDS None chromosome 1694562 1695245 + Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) False
CAC1637 CAC1637 CDS None chromosome 1778703 1779014 + Hypothetical protein, CF-12 family (NCBI ptt file) False
CAC1870 CAC1870 CDS None chromosome 2017790 2018065 + Hypothetical protein (NCBI ptt file) False
CAC1951 CAC1951 CDS None chromosome 2068045 2069772 + Site-specific recombinases, DNA invertase Pin homolog (NCBI ptt file) False
CAC2039 CAC2039 CDS None chromosome 2144930 2146306 - Hypothetical protein, CF-5 family (NCBI ptt file) False
CAC2434 CAC2434 CDS None chromosome 2551088 2552566 - Membrane associatehistidine kinase with HAMP domain (NCBI ptt file) False
CAC2436 CAC2436 CDS None chromosome 2553263 2554465 - Uncharacterized conserved membrane protein (NCBI ptt file) False
CAC3012 CAC3012 CDS None chromosome 3151847 3153745 + ATPase component of ABC transporter, with duplicated ATPase domains (NCBI ptt file) False
CAC3194 murD CDS None chromosome 3338267 3339655 - UDP-N-acetylmuramoylalanine D-glutamate ligase (NCBI ptt file) False
CAC3220 CAC3220 CDS None chromosome 3369337 3370023 - Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) False
CAC3570 accC CDS None chromosome 3770796 3772139 - Biotin carboxylase (NCBI ptt file) False
CAC3572 accB CDS None chromosome 3772672 3773151 - Biotin carboxyl carrier protein of acetyl-CoA carboxylase (NCBI ptt file) False
CAC3703 CAC3703 CDS None chromosome 3907635 3908465 - Hypothetical protein (NCBI ptt file) False
CAC3704 CAC3704 CDS None chromosome 3908484 3910598 - Hypothetical protein, CF-7 family (NCBI ptt file) False
CAC3705 CAC3705 CDS None chromosome 3910595 3910867 - Hypothetical protein, CF-37 family(almost identical) (NCBI ptt file) False
CAC3706 CAC3706 CDS None chromosome 3910881 3911192 - Hypothetical protein, CF-12 family (NCBI ptt file) False
CAC3707 CAC3707 CDS None chromosome 3911185 3911571 - Uncharacterized protein, homolog of Bacillus firmus (gi:2654481) (NCBI ptt file) False
CAC3708 CAC3708 CDS None chromosome 3911568 3912026 - Hypothetical protein (NCBI ptt file) False
CAC3709 CAC3709 CDS None chromosome 3912019 3916515 - DNA segregation ATPase, FtsK/SpoIIIE family, YUKA B.subtilis ortholog (NCBI ptt file) False
CAC3710 CAC3710 CDS None chromosome 3916525 3917640 - Uncharacterized protein, YUKC B.subtilis homolog (NCBI ptt file) False
CAC3711 CAC3711 CDS None chromosome 3917627 3917899 - Hypothetical protein (NCBI ptt file) False
CAC3712 CAC3712 CDS None chromosome 3917883 3918425 - Hypothetical protein (NCBI ptt file) False
CAC3713 CAC3713 CDS None chromosome 3918403 3918693 - Uncharacterized conserved protein, yukE/yfjA B.subtilis 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 44

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.