Organism : Geobacter sulfurreducens | Module List:
Module 79 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 79

There are 9 regulatory influences for Module 79

Regulator Table (9)
Regulator Name Type
GSU2915 tf
GSU3217 tf
GSU0063 tf
GSU1115 tf
GSU2809 tf
GSU1992 tf
GSU2868 tf
GSU1250 tf
GSU2041 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
2318 4.90e+01 AAGAAt.tt.C.gttatgccgAaa
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2319 2.00e+04 GCtGgCGCaGatGGGCgTc
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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 79 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Signal Transduction kegg subcategory 6.01e-03 1.91e-02 3/29
Two-component system kegg pathway 6.01e-03 1.91e-02 3/29
Cellular Processes kegg category 5.53e-03 1.84e-02 3/29
Cell Motility kegg subcategory 5.53e-03 1.84e-02 3/29
Bacterial chemotaxis kegg pathway 1.30e-03 8.43e-03 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 9.26e-03 1.68e-02 6/29
Cell motility cog subcategory 3.22e-03 6.14e-03 4/29
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 79

There are 29 genes in Module 79

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0063 GSU0063 CDS None chromosome 79477 79698 + conserved hypothetical protein (VIMSS) True
GSU0225 GSU0225 CDS None chromosome 232553 232768 + hypothetical protein (VIMSS) False
GSU0314 GSU0314 CDS None chromosome 345463 346566 + general secretion protein E N-terminal domain protein (NCBI) False
GSU0435 GSU0435 CDS None chromosome 466122 467771 + MSHA biogenesis protein MshE, putative (VIMSS) False
GSU0683 GSU0683 CDS None chromosome 718970 720676 + methyl-accepting chemotaxis protein, putative (VIMSS) False
GSU0691 GSU0691 CDS None chromosome 730972 731337 - translation initation factor SUI1, putative (NCBI) False
GSU0701 GSU0701 CDS None chromosome 743438 744721 + cytochrome c family protein (NCBI) False
GSU0820 sppA-1 CDS None chromosome 880374 881339 + signal peptide peptidase SppA, 36K type (NCBI) False
GSU0900 GSU0900 CDS None chromosome 966579 967520 - hypothetical protein (VIMSS) False
GSU1302 GSU1302 CDS None chromosome 1423689 1426196 + sensor histidine kinase/response regulator (VIMSS) False
GSU1327 GSU1327 CDS None chromosome 1452599 1453555 + homocysteine S-methyltransferase domain protein (VIMSS) False
GSU1418 GSU1418 CDS None chromosome 1555933 1556283 - hypothetical protein (VIMSS) False
GSU1570 GSU1570 CDS None chromosome 1722702 1723646 + membrane protein, TerC family (NCBI) False
GSU1572 GSU1572 CDS None chromosome 1725013 1725540 + ribD domain protein (NCBI) False
GSU2095 GSU2095 CDS None chromosome 2302816 2304084 - NADH oxidase, putative (VIMSS) False
GSU2173 GSU2173 CDS None chromosome 2385179 2385307 + lipoprotein, putative (VIMSS) False
GSU2289 GSU2289 CDS None chromosome 2506846 2508291 + nicotinate phosphoribosyltransferase, putative (NCBI) False
GSU2358 GSU2358 CDS None chromosome 2577762 2579654 + isoamylase family protein (VIMSS) False
GSU2360 GSU2360 CDS None chromosome 2582132 2585122 + maltooligosyltrehalose synthase, putative (VIMSS) False
GSU2369 GSU2369 CDS None chromosome 2596912 2597085 + hypothetical protein (VIMSS) False
GSU2384 GSU2384 CDS None chromosome 2612913 2614757 - sensor histidine kinase (VIMSS) False
GSU2416 cheW-8 CDS None chromosome 2650477 2650977 + chemotaxis protein CheW (NCBI) False
GSU2453 GSU2453 CDS None chromosome 2692625 2693677 - membrane protein, putative (VIMSS) False
GSU2510 GSU2510 CDS None chromosome 2768336 2769262 + hypothetical protein (VIMSS) False
GSU2531 GSU2531 CDS None chromosome 2791476 2794637 - sensory box histidine kinase (VIMSS) False
GSU2578 cheW-9 CDS None chromosome 2840026 2840406 - purine-binding chemotaxis protein CheW (NCBI) False
GSU2582 GSU2582 CDS None chromosome 2844240 2845544 + hypothetical protein (VIMSS) False
GSU2646 GSU2646 CDS None chromosome 2917145 2917477 + hypothetical protein (VIMSS) False
GSU2931 GSU2931 CDS None chromosome 3228374 3228838 + 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 79

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.