Organism : Geobacter sulfurreducens | Module List:
Module 278 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 278

There are 6 regulatory influences for Module 278

Regulator Table (6)
Regulator Name Type
GSU2915 tf
GSU1495 tf
GSU2202 tf
GSU2177 tf
GSU2523 tf
GSU1569 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
2716 1.10e+03 aCAggAAagGAgAA
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2717 5.30e+03 TTAAC.TTAaTttTaaT
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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 278 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 8.58e-03 2.41e-02 3/32
Two-component system kegg pathway 8.58e-03 2.41e-02 3/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 3.06e-02 4.96e-02 11/32
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 278

There are 32 genes in Module 278

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0273 GSU0273 CDS None chromosome 280807 282576 + radical SAM domain protein (NCBI) False
GSU0295 cheR-1 CDS None chromosome 323955 324788 - chemotaxis protein methyltransferase CheR (NCBI) False
GSU0314 GSU0314 CDS None chromosome 345463 346566 + general secretion protein E N-terminal domain protein (NCBI) False
GSU0413 fliI CDS None chromosome 444236 445561 + flagellum-specific ATP synthase FliI (NCBI) False
GSU0427 GSU0427 CDS None chromosome 456466 456936 - lipoprotein, putative (VIMSS) False
GSU0428 GSU0428 CDS None chromosome 457223 457777 + lipoprotein, putative (VIMSS) False
GSU0432 GSU0432 CDS None chromosome 461302 462294 + conserved hypothetical protein (VIMSS) False
GSU0512 GSU0512 CDS None chromosome 545697 547337 + conserved hypothetical protein (VIMSS) False
GSU0705 GSU0705 CDS None chromosome 752867 753697 + cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) False
GSU0758 GSU0758 CDS None chromosome 808948 809634 + membrane protein, putative (VIMSS) False
GSU0759 GSU0759 CDS None chromosome 809874 811532 - hypothetical protein (VIMSS) False
GSU0833 GSU0833 CDS None chromosome 894388 894627 - hypothetical protein (VIMSS) False
GSU1042 GSU1042 CDS None chromosome 1129240 1129644 + conserved hypothetical protein (NCBI) False
GSU1156 asnS CDS None chromosome 1261648 1263033 + asparaginyl-tRNA synthetase (NCBI) False
GSU1164 GSU1164 CDS None chromosome 1268258 1269421 + ABC transporter, permease protein (VIMSS) False
GSU1281 nikO CDS None chromosome 1396577 1397326 + component of nickel ABC transport system (Dmitry Rodionov) False
GSU1391 GSU1391 CDS None chromosome 1519957 1520541 + Fic family protein (NCBI) False
GSU1611 GSU1611 CDS None chromosome 1762910 1766008 + AcrB/AcrD/AcrF family protein (VIMSS) False
GSU1991 GSU1991 CDS None chromosome 2184557 2185285 + CAAX amino terminal protease family protein (NCBI) False
GSU2114 GSU2114 CDS None chromosome 2332492 2332875 - hypothetical protein (VIMSS) False
GSU2117 GSU2117 CDS None chromosome 2335443 2335727 + hypothetical protein (VIMSS) False
GSU2123 GSU2123 CDS None chromosome 2342182 2343495 + HD domain protein (NCBI) False
GSU2163 GSU2163 CDS None chromosome 2376777 2377046 + hypothetical protein (VIMSS) False
GSU2274 fbP-2 CDS None chromosome 2491287 2491703 - FKBP-type peptidyl-prolyl cis-trans isomerase (NCBI) False
GSU2295 GSU2295 CDS None chromosome 2512972 2513466 - hypothetical protein (VIMSS) False
GSU2385 GSU2385 CDS None chromosome 2614738 2615343 - hypothetical protein (VIMSS) False
GSU2402 GSU2402 CDS None chromosome 2638003 2638584 + hypothetical protein (VIMSS) False
GSU2533 GSU2533 CDS None chromosome 2795087 2796298 - hypothetical protein (VIMSS) False
GSU2782 GSU2782 CDS None chromosome 3060587 3063697 + AcrB/AcrD/AcrF family protein (VIMSS) False
GSU3031 GSU3031 CDS None chromosome 3337484 3339019 + sigma-54 dependent transcriptional regulator (VIMSS) False
GSU3118 regX3 CDS None chromosome 3420191 3420874 - DNA-binding response regulator (NCBI) False
GSU3119 GSU3119 CDS None chromosome 3420871 3422421 - sensor histidine kinase (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 278

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.