Organism : Clostridium acetobutylicum | Module List:
Module 137 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 137

There are 11 regulatory influences for Module 137

Regulator Table (11)
Regulator Name Type
CAC1766 tf
CAC0549 tf
CAC3199 tf
CAC3603 tf
CAC0183 tf
CAC1465 tf
CAC2842 tf
CAC1965 tf
CAC3579 tf
CAC3669 tf
CAC1675 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
6926 5.30e+00 AAGggGca
Loader icon
6927 5.90e+03 GGaGCG
Loader icon
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 137 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 137

There are 27 genes in Module 137

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0080 agrC CDS None chromosome 87617 88960 + Histidine kinase-like ATPase (NCBI ptt file) False
CAC0252 CAC0252 CDS None chromosome 282379 283338 - Molybdate-binding protein (NCBI ptt file) False
CAC0317 CAC0317 CDS None chromosome 370955 372451 + Sensory transduction histidine kinase (NCBI ptt file) False
CAC0336 CAC0336 CDS None chromosome 396432 396956 + Hypothetical protein, CF-22 family (NCBI ptt file) False
CAC0485 CAC0485 CDS None chromosome 560374 561225 + TRNA-processing ribonuclease BN (NCBI ptt file) False
CAC0703 CAC0703 CDS None chromosome 812161 813705 + Sugar ABC-transporter, ATP-ase component (NCBI ptt file) False
CAC0753 CAC0753 CDS None chromosome 876426 877517 + PolyA polymerase related protein (HD hydrolase) and P-loop ATP-ase domain (NCBI ptt file) False
CAC0839 potB CDS None chromosome 969194 970027 - ABC-type spermidine/putrescine transport system, permease component I (NCBI ptt file) False
CAC1125 CAC1125 CDS None chromosome 1292081 1292542 - Hypothetical protein (NCBI ptt file) False
CAC1194 CAC1194 CDS None chromosome 1342955 1343371 + Hypothetical protein (NCBI ptt file) False
CAC1284 prmA CDS None chromosome 1428812 1429747 + SAM-dependent methyltransferase (NCBI ptt file) False
CAC1352 CAC1352 CDS None chromosome 1495896 1497602 - Membrane associated chemotaxis sensory transducer protein (MSP domain and HAMP domain) (NCBI ptt file) False
CAC1465 CAC1465 CDS None chromosome 1615920 1616339 + Transcriptional regulator, MarR/EmrR family (NCBI ptt file) True
CAC1496 CAC1496 CDS None chromosome 1640953 1641972 + Uncharacterized protein, homolog of YCGL B.subtilis (NCBI ptt file) False
CAC1607 CAC1607 CDS None chromosome 1750067 1750342 - Hypothetical protein (NCBI ptt file) False
CAC1631 CAC1631 CDS None chromosome 1772851 1773903 + Biotin synthase family enzyme (NCBI ptt file) False
CAC1845 motB CDS None chromosome 1996855 1997619 - Flagellar motor protein MotB (NCBI ptt file) False
CAC2344 CAC2344 CDS None chromosome 2455007 2456113 - LPS biosynthesis protein , RfbU family (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
CAC2400 CAC2400 CDS None chromosome 2511267 2511800 + Serine/threonine kinase related protein, inactivated (HRDL motif absent) (fragment) (NCBI ptt file) False
CAC2690 CAC2690 CDS None chromosome 2813051 2813866 - Transcriptional regulator, LysR family (NCBI ptt file) True
CAC2874 CAC2874 CDS None chromosome 3007468 3008625 - UDP-N-acetylglucosamine 2-epimerase (NCBI ptt file) False
CAC2893 CAC2893 CDS None chromosome 3027579 3027866 - Hypothetical protein (NCBI ptt file) False
CAC2978 gatC CDS None chromosome 3114382 3114675 - Glu-tRNA amidotransferase, subunit C (NCBI ptt file) False
CAC3257 CAC3257 CDS None chromosome 3408207 3408575 - Predicted membrane protein (NCBI ptt file) False
CAC3493 CAC3493 CDS None chromosome 3689655 3690095 - Predicted transcriptional regulator component, YOBU B.subtilis homolog (NCBI ptt file) False
CAC3669 CAC3669 CDS None chromosome 3870221 3870682 - Transcriptional regulator, MarR/EmrR 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 137

Please add your comments for this module by using the form below. Your comments will be publicly available.

comments powered by Disqus
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.