Organism : Clostridium acetobutylicum | Module List:
Module 142 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 142

There are 12 regulatory influences for Module 142

Regulator Table (12)
Regulator Name Type
CAC1430 tf
CAC1696 tf
CAC2486 tf
CAC0693 tf
CAC2859 tf
CAC0201 tf
CAC3481 tf
CAC0195 tf
CAC0768 tf
CAC0197 tf
CAC1689 tf
CAC3502 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
6936 6.30e-13 GGaGGa
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6937 1.80e-04 G.cACAAAaAtGTgcgTaCTTga
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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 142 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 1.28e-02 2.17e-02 3/28
Carbohydrate transport and metabolism cog subcategory 1.19e-03 2.31e-03 6/28
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 142

There are 28 genes in Module 142

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0146 CAC0146 CDS None chromosome 150796 151983 - Related to ABC transporter permease component (NCBI ptt file) False
CAC0147 CAC0147 CDS None chromosome 151964 152920 - ABC transporter, ATP-binding protein (NCBI ptt file) False
CAC0195 CAC0195 CDS None chromosome 221433 221780 - Predicted transcriptional regulator (NCBI ptt file) True
CAC0196 CAC0196 CDS None chromosome 221908 222963 + NADH-dependent flavine oxidoreductase (NCBI ptt file) False
CAC0738 CAC0738 CDS None chromosome 856676 857596 + DNA polymerase III epsilon subunit (3'-5' exonuclease) containing BRCT domain (NCBI ptt file) False
CAC0739 CAC0739 CDS None chromosome 857808 858914 + Predicted membrane protein (NCBI ptt file) False
CAC1341 araD CDS None chromosome 1480333 1481034 + Ribulose-5-phosphate 4-epimerase family protein (NCBI ptt file) False
CAC1342 araA CDS None chromosome 1481052 1482518 + L-arabinose isomerase (NCBI ptt file) False
CAC1348 CAC1348 CDS None chromosome 1490878 1492869 + Transketolase, TKT (NCBI ptt file) False
CAC1349 galM CDS None chromosome 1492885 1493922 + Aldose-1-epimerase (NCBI ptt file) False
CAC1430 CAC1430 CDS None chromosome 1574943 1575683 + Transcriptional regulators of sugar metabolism (deoR family) (NCBI ptt file) True
CAC1484 CAC1484 CDS None chromosome 1631169 1631687 + Nitroreductase family protein (NCBI ptt file) False
CAC1627 gyrB CDS None chromosome 1766134 1768086 + DNA gyrase B subunit (NCBI ptt file) False
CAC1662 CAC1662 CDS None chromosome 1805610 1806107 + Hypothetical protein (NCBI ptt file) False
CAC1684 CAC1684 CDS None chromosome 1833236 1835053 + TYPA/BIPA type GTPase (NCBI ptt file) False
CAC1697 CAC1697 CDS None chromosome 1848579 1848842 + Uncharacterized conserved protein, YMXH B.subtilis homolog (NCBI ptt file) False
CAC1811 CAC1811 CDS None chromosome 1959996 1960676 + Periplasmic serine protease, YMFB B.subtilis ortholog (NCBI ptt file) False
CAC2459 CAC2459 CDS None chromosome 2574482 2576158 - 2-oxoacid:ferredoxin oxidoreductase, alpha subunit (NCBI ptt file) False
CAC2584 CAC2584 CDS None chromosome 2688963 2690408 - Protein containing ChW-repeats (NCBI ptt file) False
CAC3031 hisC CDS None chromosome 3172870 3173928 - Histidinol-phosphate aminotransferase (NCBI ptt file) False
CAC3077 CAC3077 CDS None chromosome 3227206 3228828 - Uncharacterized FAD-dependent dehydrogenase (NCBI ptt file) False
CAC3078 CAC3078 CDS None chromosome 3228844 3230055 - Uncharacterized secreted protein, YBBR Bacillus subtilis homolog (NCBI ptt file) False
CAC3194 murD CDS None chromosome 3338267 3339655 - UDP-N-acetylmuramoylalanine D-glutamate ligase (NCBI ptt file) False
CAC3204 CAC3204 CDS None chromosome 3350269 3351654 - Cell cycle protein MesJ ortholog, ATPase of the PP-loop superamily (NCBI ptt file) False
CAC3334 CAC3334 CDS None chromosome 3507964 3508500 - Multimeric flavodoxin WrbA family protein (NCBI ptt file) False
CAC3452 xynD CDS None chromosome 3647630 3649231 + Beta-xylosidase, family 43 glycosyl hydrolase (NCBI ptt file) False
CAC3454 CAC3454 CDS None chromosome 3651191 3652126 - Predicted TIM-barrel enzyme, nifR3 family (NCBI ptt file) False
CAC3594 CAC3594 CDS None chromosome 3796638 3797834 - Glycosyltransferase (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 142

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.