Organism : Geobacter sulfurreducens | Module List:
Module 59 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 59

There are 10 regulatory influences for Module 59

Regulator Table (10)
Regulator Name Type
GSU0164 tf
GSU1250 tf
GSU3370 tf
GSU0018 tf
GSU0300 tf
GSU2185 tf
GSU3108 tf
GSU1569 tf
GSU2041 tf
GSU1115 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
2278 5.90e-02 aaaACAaAActTtATTTtAT
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2279 1.80e+01 tccgGCtgtttcTttcc.aa
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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 59 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 1.57e-03 9.28e-03 4/34
Two-component system kegg pathway 1.57e-03 9.28e-03 4/34
Cellular Processes kegg category 1.42e-03 8.78e-03 4/34
Cell Motility kegg subcategory 1.42e-03 8.78e-03 4/34
Bacterial chemotaxis kegg pathway 2.28e-04 2.82e-03 4/34

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 2.05e-02 3.46e-02 5/34
Chemotaxis signal transduction protein cog 3.00e-06 1.00e-05 3/34
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 59

There are 34 genes in Module 59

Gene Member Table (34)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0124 GSU0124 CDS None chromosome 138515 139231 - competence protein F, putative (VIMSS) False
GSU0134 GSU0134 CDS None chromosome 148677 149777 - metallo-beta-lactamase family protein (NCBI) False
GSU0235 GSU0235 CDS None chromosome 242523 244808 - S1 RNA binding domain protein (VIMSS) False
GSU0258 GSU0258 CDS None chromosome 266599 266805 - hypothetical protein (VIMSS) False
GSU0269 GSU0269 CDS None chromosome 276219 276533 + conserved hypothetical protein (VIMSS) False
GSU0597 GSU0597 CDS None chromosome 628093 628335 - hypothetical protein (VIMSS) False
GSU0855 GSU0855 CDS None chromosome 914623 915558 - membrane protein, TerC family (NCBI) False
GSU1025 GSU1025 CDS None chromosome 1104518 1105120 - conserved domain protein (NCBI) False
GSU1299 cheW CDS None chromosome 1420264 1420758 + purine-binding chemotaxis protein CheW (NCBI) False
GSU1372 GSU1372 CDS None chromosome 1500642 1501502 - 3-hydroxyisobutyrate dehydrogenase family protein (VIMSS) False
GSU1373 GSU1373 CDS None chromosome 1501493 1501606 + hypothetical protein (VIMSS) False
GSU1618 GSU1618 CDS None chromosome 1771700 1772563 - hypothetical protein (VIMSS) False
GSU1619 cheY-4 CDS None chromosome 1772610 1772969 - chemotaxis protein CheY (NCBI) False
GSU1620 GSU1620 CDS None chromosome 1773123 1775249 - iron-sulfur cluster binding protein, putative (VIMSS) False
GSU1621 GSU1621 CDS None chromosome 1775253 1775891 - conserved domain protein (VIMSS) False
GSU1622 GSU1622 CDS None chromosome 1776004 1777953 + L-lactate permease (VIMSS) False
GSU1623 GSU1623 CDS None chromosome 1778047 1779420 + glycolate oxidase subunit GlcD, putative (VIMSS) False
GSU1624 GSU1624 CDS None chromosome 1779431 1780681 + glycolate oxidase iron-sulfur subunit, putative (NCBI) False
GSU1671 GSU1671 CDS None chromosome 1831449 1832417 - response regulator/GGDEF domain protein (NCBI) False
GSU1680 GSU1680 CDS None chromosome 1841476 1841907 - conserved hypothetical protein (VIMSS) False
GSU1751 GSU1751 CDS None chromosome 1915160 1915306 - hypothetical protein (VIMSS) False
GSU2077 GSU2077 CDS None chromosome 2283949 2284191 + hypothetical protein (VIMSS) False
GSU2125 GSU2125 CDS None chromosome 2344357 2345841 + conserved domain protein (VIMSS) False
GSU2135 GSU2135 CDS None chromosome 2350205 2353309 - heavy metal efflux pump, CzcA family (VIMSS) False
GSU2218 cheW-6 CDS None chromosome 2434005 2434481 - chemotaxis protein CheW (NCBI) False
GSU2334 GSU2334 CDS None chromosome 2553794 2553901 + hypothetical protein (VIMSS) False
GSU2369 GSU2369 CDS None chromosome 2596912 2597085 + hypothetical protein (VIMSS) False
GSU2416 cheW-8 CDS None chromosome 2650477 2650977 + chemotaxis protein CheW (NCBI) False
GSU2450 GSU2450 CDS None chromosome 2689027 2689803 - conserved hypothetical protein (VIMSS) False
GSU2452 GSU2452 CDS None chromosome 2690239 2692632 - copper-translocating P-type ATPase (VIMSS) False
GSU2454 GSU2454 CDS None chromosome 2693681 2694721 - membrane protein, putative (VIMSS) False
GSU2477 GSU2477 CDS None chromosome 2717042 2719636 + TPR domain/radical SAM/B12 binding domain protein (NCBI) False
GSU2973 GSU2973 CDS None chromosome 3265018 3265431 - lipoprotein, putative (VIMSS) False
GSU3417 GSU3417 CDS None chromosome 3759521 3761050 + dioxygenase, putative (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 59

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.