Organism : Geobacter sulfurreducens | Module List:
Module 287 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 287

There are 12 regulatory influences for Module 287

Regulator Table (12)
Regulator Name Type
GSU3217 tf
GSU2587 tf
GSU2041 tf
GSU0812 tf
GSU2787 tf
GSU2779 tf
GSU3363 tf
GSU2868 tf
GSU0063 tf
GSU0735 tf
GSU2581 tf
GSU2716 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
2732 1.00e+01 gTAAAAat.aCCCacT
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2733 1.10e+03 tT.TTCcTCTagccTAacCaacCt
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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 287 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 1.58e-02 3.60e-02 4/28
Signal Transduction kegg subcategory 5.28e-03 1.78e-02 3/28
Two-component system kegg pathway 5.28e-03 1.78e-02 3/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Replication, recombination and repair cog subcategory 1.95e-03 3.82e-03 4/28
Signal transduction mechanisms cog subcategory 1.74e-03 3.42e-03 7/28
Cell motility cog subcategory 1.64e-02 2.83e-02 3/28
Inorganic ion transport and metabolism cog subcategory 2.24e-02 3.75e-02 3/28
Methyl-accepting chemotaxis protein cog 9.80e-05 2.51e-04 3/28
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 287

There are 28 genes in Module 287

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0048 GSU0048 CDS None chromosome 63072 63908 + integrase (NCBI) False
GSU0270 glmS CDS None chromosome 276632 278461 - glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (NCBI) False
GSU0547 mutS2 CDS None chromosome 579087 581465 + MutS2 family protein (NCBI) False
GSU0549 GSU0549 CDS None chromosome 583123 583803 + conserved domain protein (NCBI) False
GSU0582 GSU0582 CDS None chromosome 613603 615693 + methyl-accepting chemotaxis protein (VIMSS) False
GSU0605 thiD CDS None chromosome 639288 640760 - thiamine-phosphate pyrophosphorylase/phosphomethylpyrimidine kinase (NCBI) False
GSU0901 fragment CDS None chromosome 967566 968357 + conserved domain protein (NCBI) False
GSU0916 GSU0916 CDS None chromosome 982110 983294 - methyl-accepting chemotaxis protein (VIMSS) False
GSU1029 GSU1029 CDS None chromosome 1107913 1109562 + methyl-accepting chemotaxis protein (VIMSS) False
GSU1034 GSU1034 DUMMY None chromosome 0 0 + None False
GSU1101 GSU1101 CDS None chromosome 1185871 1187484 - sensory box histidine kinase (VIMSS) False
GSU1383 dnaQ CDS None chromosome 1511698 1512243 + exonuclease (NCBI) False
GSU1552 GSU1552 CDS None chromosome 1704642 1705172 + conserved hypothetical protein (VIMSS) False
GSU1567 htpX CDS None chromosome 1721015 1721875 + peptidase, M48 family (NCBI) False
GSU1742 GSU1742 CDS None chromosome 1906918 1908549 - Na/Pi-cotransporter family protein (VIMSS) False
GSU2094 GSU2094 CDS None chromosome 2301233 2302222 - response regulator (VIMSS) False
GSU2300 GSU2300 CDS None chromosome 2519819 2519935 + hypothetical protein (VIMSS) False
GSU2441 GSU2441 CDS None chromosome 2674961 2675707 - conserved hypothetical protein (VIMSS) False
GSU2574 GSU2574 CDS None chromosome 2835091 2836197 - response regulator (VIMSS) False
GSU2594 GSU2594 CDS None chromosome 2859387 2860181 + ISGsu6, transposase OrfB (VIMSS) False
GSU2659 GSU2659 CDS None chromosome 2931410 2931631 + hypothetical protein (VIMSS) False
GSU2661 GSU2661 CDS None chromosome 2932127 2932693 + conserved hypothetical protein (VIMSS) False
GSU2759 GSU2759 CDS None chromosome 3038707 3040590 - potassium efflux system protein (VIMSS) False
GSU2984 znuC CDS None chromosome 3275601 3276419 - permease component of zinc ABC transporter (Dmitry Rodionov) False
GSU3150 GSU3150 CDS None chromosome 3457827 3458321 - HPP family protein (NCBI) False
GSU3217 GSU3217 CDS None chromosome 3522478 3523983 + sigma-54 dependent DNA-binding response regulator (VIMSS) True
GSU3224 GSU3224 CDS None chromosome 3535172 3537139 + hypothetical protein (VIMSS) False
GSU3372 GSU3372 CDS None chromosome 3705606 3707048 - cardiolipin synthetase, 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 287

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.