Organism : Geobacter sulfurreducens | Module List:
Module 337 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 337

There are 19 regulatory influences for Module 337

Regulator Table (19)
Regulator Name Type
GSU3217 tf
GSU0267 tf
GSU0473 tf
GSU0598 tf
GSU1003 tf
GSU1382 tf
GSU2149 tf
GSU0300 tf
GSU3108 tf
GSU1617 tf
GSU1992 tf
GSU0399 tf
GSU0735 tf
GSU1095 tf
GSU0951 tf
GSU0812 tf
GSU1428 tf
GSU0625 tf
GSU2506 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
2830 5.00e+02 AAgaGcAagGAgatGcccGAT
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2831 1.10e+05 GGCATTaTTCTTcAT
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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 337 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 337

There are 31 genes in Module 337

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0059 GSU0059 CDS None chromosome 77772 78041 - hypothetical protein (VIMSS) False
GSU0532 GSU0532 CDS None chromosome 565957 566235 - conserved domain protein (VIMSS) False
GSU0595 GSU0595 CDS None chromosome 627368 627616 + hypothetical protein (NCBI) False
GSU0764 GSU0764 CDS None chromosome 819660 819761 + hypothetical protein (VIMSS) False
GSU0819 GSU0819 CDS None chromosome 879571 880329 + conserved hypothetical protein (VIMSS) False
GSU1031 GSU1031 CDS None chromosome 1111462 1111602 + hypothetical protein (VIMSS) False
GSU1032 GSU1032 CDS None chromosome 1111658 1113595 + methyl-accepting chemotaxis protein (VIMSS) False
GSU1092 GSU1092 CDS None chromosome 1177364 1179052 - GH3 auxin-responsive promoter family protein (NCBI) False
GSU1093 GSU1093 CDS None chromosome 1179049 1180134 - hypothetical protein (VIMSS) False
GSU1094 GSU1094 CDS None chromosome 1180164 1180304 - hypothetical protein (VIMSS) False
GSU1100 GSU1100 CDS None chromosome 1185246 1185683 - hypothetical protein (NCBI) False
GSU1296 GSU1296 CDS None chromosome 1414746 1416926 + sensory box histidine kinase/response regulator (VIMSS) False
GSU2153 GSU2153 CDS None chromosome 2369779 2369988 + hypothetical protein (VIMSS) False
GSU2154 GSU2154 CDS None chromosome 2370002 2370976 + hypothetical protein (VIMSS) False
GSU2205 GSU2205 CDS None chromosome 2420518 2420826 + hypothetical protein (VIMSS) False
GSU2418 GSU2418 CDS None chromosome 2651489 2652439 + nickel-dependent hydrogenase, small subunit, putative (VIMSS) False
GSU2511 GSU2511 CDS None chromosome 2769311 2771932 - sensory box/GGDEF family protein (VIMSS) False
GSU2591 GSU2591 CDS None chromosome 2855722 2856504 + ISGsu5, transposase (VIMSS) False
GSU2658 GSU2658 CDS None chromosome 2931002 2931232 + lipoprotein, putative (VIMSS) False
GSU2672 GSU2672 CDS None chromosome 2947371 2947847 + hypothetical protein (VIMSS) False
GSU3028 motB CDS None chromosome 3332063 3332863 + chemotaxis MotB protein (NCBI) False
GSU3168 GSU3168 CDS None chromosome 3476577 3477770 + beta-ketoacyl synthase domain protein (NCBI) False
GSU3219 GSU3219 CDS None chromosome 3525819 3531911 + fibronectin type III domain protein (VIMSS) False
GSU3224 GSU3224 CDS None chromosome 3535172 3537139 + hypothetical protein (VIMSS) False
GSU3226 GSU3226 CDS None chromosome 3538273 3540003 + cytochrome c family protein (NCBI) False
GSU3232 GSU3232 CDS None chromosome 3546769 3547101 + cytochrome c family protein, putative (NCBI) False
GSU3233 GSU3233 CDS None chromosome 3547120 3550323 + cytochrome c family protein (VIMSS) False
GSU3234 GSU3234 CDS None chromosome 3550468 3550614 + hypothetical protein (VIMSS) False
GSU3398 GSU3398 CDS None chromosome 3737064 3738368 + metal ion efflux outer membrane protein family protein, putative (VIMSS) False
GSU3399 GSU3399 CDS None chromosome 3738371 3740119 + efflux transporter, RND family, MFP subunit (NCBI) False
GSU3400 GSU3400 CDS None chromosome 3740132 3743203 + heavy metal efflux pump, CzcA family (VIMSS) 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 337

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.