Organism : Geobacter sulfurreducens | Module List:
Module 126 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 126

There are 9 regulatory influences for Module 126

Regulator Table (9)
Regulator Name Type
GSU1687 tf
GSU3421 tf
GSU2262 tf
GSU0770 tf
GSU1992 tf
GSU0514 tf
GSU1989 tf
GSU0551 tf
GSU1692 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
2412 8.80e+02 CtCctGgGGggcCGg
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2413 5.60e+03 TctCcaTtTtTcCCT
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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 126 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Energy Metabolism kegg subcategory 6.08e-03 1.93e-02 4/31
Environmental Information Processing kegg category 2.39e-02 4.79e-02 4/31
Signal Transduction kegg subcategory 7.65e-03 2.24e-02 3/31
Two-component system kegg pathway 7.65e-03 2.24e-02 3/31
Cellular Processes kegg category 7.06e-03 2.13e-02 3/31
Cell Motility kegg subcategory 7.06e-03 2.13e-02 3/31
Bacterial chemotaxis kegg pathway 1.68e-03 9.66e-03 3/31
Microbial metabolism in diverse environments kegg pathway 1.60e-02 3.63e-02 3/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.10e-02 1.98e-02 13/31
Cell motility cog subcategory 2.32e-02 3.87e-02 3/31
Energy production and conversion cog subcategory 6.06e-04 1.27e-03 7/31
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 126

There are 31 genes in Module 126

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0087 GSU0087 CDS None chromosome 98008 99012 - heterodisulfide reductase, iron-sulfur binding subunit, putative (VIMSS) False
GSU0089 GSU0089 CDS None chromosome 100019 100519 - heterodisulfide reductase subunit (VIMSS) False
GSU0090 GSU0090 CDS None chromosome 100519 102516 - heterodisulfide reductase subunit (VIMSS) False
GSU0091 GSU0091 CDS None chromosome 102517 103407 - heterodisulfide reductase subunit (VIMSS) False
GSU0213 GSU0213 CDS None chromosome 222018 223307 + radical SAM domain protein (NCBI) False
GSU0226 GSU0226 CDS None chromosome 232930 234558 + L-lactate permease, putative (VIMSS) False
GSU0526 GSU0526 CDS None chromosome 560342 560863 - conserved hypothetical protein (VIMSS) False
GSU0825 GSU0825 CDS None chromosome 885519 886427 + pirin family protein (VIMSS) False
GSU0860 GSU0860 CDS None chromosome 919385 920290 - methylenetetrahydrofolate reductase family protein (VIMSS) False
GSU0862 folD-2 CDS None chromosome 920953 921810 - folD bifunctional protein (NCBI) False
GSU0903 GSU0903 DUMMY None chromosome 0 0 + None False
GSU1053 GSU1053 CDS None chromosome 1140250 1141311 - sensory box protein (VIMSS) False
GSU1124 coaBC CDS None chromosome 1208341 1209540 + phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase (NCBI) False
GSU1180 ftsH-1 CDS None chromosome 1286588 1288441 + cell division protein FtsH (NCBI) False
GSU1274 GSU1274 CDS None chromosome 1389118 1390077 + radical SAM domain protein (NCBI) False
GSU1298 GSU1298 CDS None chromosome 1418548 1420254 + methyl-accepting chemotaxis protein (VIMSS) False
GSU1377 GSU1377 CDS None chromosome 1505701 1506483 - 3-hydroxybutyryl-CoA dehydratase (VIMSS) False
GSU1461 pyrF CDS None chromosome 1601706 1602425 + orotidine 5`-phosphate decarboxylase (NCBI) False
GSU1535 recD CDS None chromosome 1687048 1688835 + exodeoxyribonuclease V, alpha subunit (NCBI) False
GSU1710 GSU1710 DUMMY None chromosome 0 0 + None False
GSU2047 GSU2047 CDS None chromosome 2246279 2247466 - conserved hypothetical protein (VIMSS) False
GSU2050 secA CDS None chromosome 2249292 2251985 - preprotein translocase, SecA subunit (NCBI) False
GSU2102 GSU2102 CDS None chromosome 2314210 2315106 - pyruvate formate-lyase-activating enzyme, putative (VIMSS) False
GSU2214 cheB-3 CDS None chromosome 2429043 2430158 - protein-glutamate methylesterase (NCBI) False
GSU2222 cheA-2 CDS None chromosome 2436546 2438624 - chemotaxis protein CheA (NCBI) False
GSU2272 GSU2272 CDS None chromosome 2489013 2490224 - lipoprotein, putative (VIMSS) False
GSU2375 GSU2375 DUMMY None chromosome 0 0 + None False
GSU2879 leuB CDS None chromosome 3154503 3155591 - 3-isopropylmalate dehydrogenase (NCBI) False
GSU3062 GSU3062 CDS None chromosome 3366639 3368330 - radical SAM domain protein (NCBI) False
GSU3260 GSU3260 CDS None chromosome 3575462 3576535 + phosphoserine aminotransferase, putative (VIMSS) False
GSU3421 GSU3421 CDS None chromosome 3766220 3766945 - transcriptional regulator, Crp/Fnr family (VIMSS) True

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 126

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.