Organism : Geobacter sulfurreducens | Module List:
Module 82 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 82

There are 7 regulatory influences for Module 82

Regulator Table (7)
Regulator Name Type
GSU0951 tf
GSU2354 tf
GSU0300 tf
GSU2506 tf
GSU1940 tf
GSU1863 tf
GSU3053 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
2324 1.30e+00 aAttaTtgtataTCaATATcaacT
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2325 8.10e+01 c.AtCAtGaagAaCc
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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 82 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Environmental Information Processing kegg category 2.10e-02 4.37e-02 4/30
Signal Transduction kegg subcategory 6.80e-03 2.08e-02 3/30
Two-component system kegg pathway 6.80e-03 2.08e-02 3/30
Cellular Processes kegg category 7.90e-05 1.35e-03 5/30
Cell Motility kegg subcategory 7.90e-05 1.35e-03 5/30
Bacterial chemotaxis kegg pathway 1.48e-03 9.08e-03 3/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
sensory_box tigrfam 1.22e-03 2.32e-03 3/30
Regulatory functions tigr mainrole 3.31e-03 5.62e-03 3/30
Small molecule interactions tigr sub1role 1.30e-03 2.46e-03 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 2.04e-03 3.98e-03 13/30
Signal transduction mechanisms cog subcategory 1.13e-04 2.83e-04 9/30
Cell motility cog subcategory 3.75e-03 7.11e-03 4/30
Intracellular trafficking, secretion, and vesicular transport cog subcategory 6.53e-03 1.21e-02 3/30
Methyl-accepting chemotaxis protein cog 1.30e-04 3.20e-04 3/30
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 82

There are 30 genes in Module 82

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0120 GSU0120 CDS None chromosome 134385 134819 - hydrogenase maturation protease (VIMSS) False
GSU0264 GSU0264 CDS None chromosome 270803 272038 - drug resistance transporter, Bcr/CflA family (VIMSS) False
GSU0275 GSU0275 CDS None chromosome 285027 285218 - hypothetical protein (VIMSS) False
GSU0278 GSU0278 CDS None chromosome 288582 289847 - outer membrane efflux protein (VIMSS) False
GSU0400 GSU0400 CDS None chromosome 430815 432464 + methyl-accepting chemotaxis protein (VIMSS) False
GSU0425 fliR CDS None chromosome 454550 455344 + flagellar biosynthesis protein FliR (NCBI) False
GSU0426 flhB CDS None chromosome 455349 456407 + flagellar biosynthetic protein FlhB (NCBI) False
GSU0766 GSU0766 CDS None chromosome 820632 822869 - methyl-accepting chemotaxis protein, putative (VIMSS) False
GSU0920 GSU0920 CDS None chromosome 985467 985715 + hypothetical protein (NCBI) False
GSU0951 GSU0951 CDS None chromosome 1023807 1024397 - transcriptional regulator, TetR family (VIMSS) True
GSU1097 pstA CDS None chromosome 1182031 1182951 - phosphate ABC transporter, permease protein (NCBI) False
GSU1294 GSU1294 CDS None chromosome 1410931 1413819 + methyl-accepting chemotaxis protein (VIMSS) False
GSU1304 GSU1304 CDS None chromosome 1428274 1429974 + methyl-accepting chemotaxis protein (VIMSS) False
GSU2160 GSU2160 CDS None chromosome 2373455 2374411 + hypothetical protein (VIMSS) False
GSU2186 GSU2186 CDS None chromosome 2395548 2396717 - conserved hypothetical protein (VIMSS) False
GSU2187 GSU2187 CDS None chromosome 2396719 2399238 - ABC transporter, permease protein (VIMSS) False
GSU2188 GSU2188 CDS None chromosome 2399235 2399933 - ABC transporter, ATP-binding protein (VIMSS) False
GSU2189 GSU2189 CDS None chromosome 2400056 2401243 + sensor histidine kinase (VIMSS) False
GSU2299 GSU2299 CDS None chromosome 2518345 2519793 + cytochrome c family protein (NCBI) False
GSU2385 GSU2385 CDS None chromosome 2614738 2615343 - hypothetical protein (VIMSS) False
GSU2388 GSU2388 CDS None chromosome 2617037 2619238 - sensory box histidine kinase (VIMSS) False
GSU2401 GSU2401 CDS None chromosome 2634831 2637878 + sensory box histidine kinase/response regulator (VIMSS) False
GSU2531 GSU2531 CDS None chromosome 2791476 2794637 - sensory box histidine kinase (VIMSS) False
GSU2535 GSU2535 CDS None chromosome 2797751 2798194 - response regulator (VIMSS) False
GSU2580 GSU2580 CDS None chromosome 2842215 2842487 - hypothetical protein (VIMSS) False
GSU2671 GSU2671 CDS None chromosome 2945693 2947300 + hypothetical protein (VIMSS) False
GSU3104 prfA CDS None chromosome 3407771 3408838 - peptide chain release factor 1 (NCBI) False
GSU3154 GSU3154 CDS None chromosome 3460814 3462286 - cytochrome c nitrite reductase, catalytic subunit NrfA, putative (VIMSS) False
GSU3221 GSU3221 CDS None chromosome 3532306 3533100 + cytochrome c family protein (NCBI) False
GSU3227 GSU3227 CDS None chromosome 3540430 3540843 + hypothetical protein (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 82

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.