Organism : Geobacter sulfurreducens | Module List:
Module 32 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 32

There are 8 regulatory influences for Module 32

Regulator Table (8)
Regulator Name Type
GSU1072 tf
GSU3108 tf
GSU1483 tf
GSU1940 tf
GSU2185 tf
GSU0963 tf
GSU0551 tf
GSU0018 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
2224 1.20e+00 AATgctATtGcTataATgCAAa
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2225 1.40e+01 AagAAAGGAGTaACt
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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 32 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 2.40e-02 4.81e-02 3/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
sss tigrfam 0.00e+00 0.00e+00 3/29
Transport and binding proteins tigr mainrole 3.22e-03 5.50e-03 3/29
Cations and iron carrying compounds tigr sub1role 5.50e-05 1.46e-04 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 1.22e-02 2.17e-02 8/29
Inorganic ion transport and metabolism cog subcategory 4.82e-03 9.05e-03 4/29
General function prediction only cog subcategory 2.34e-02 3.89e-02 5/29
Predicted membrane protein cog 0.00e+00 0.00e+00 3/29
Predicted symporter cog 0.00e+00 0.00e+00 3/29
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 32

There are 29 genes in Module 32

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0096 recR CDS None chromosome 109096 109689 + recombination protein RecR (NCBI) False
GSU0174 GSU0174 CDS None chromosome 189553 191115 - acetyl-CoA hydrolase/transferase family protein (VIMSS) False
GSU0175 GSU0175 CDS None chromosome 191349 191960 + transcriptional regulator, TetR family (VIMSS) True
GSU0229 alkK CDS None chromosome 236228 237880 + medium-chain-fatty-acid--CoA ligase (NCBI) False
GSU0261 GSU0261 CDS None chromosome 268106 269872 - sodium/hydrogen exchanger family protein (VIMSS) False
GSU0851 GSU0851 CDS None chromosome 910841 911566 + rhomboid family protein (VIMSS) False
GSU0946 GSU0946 CDS None chromosome 1016762 1019290 + sensory box/GGDEF family protein (VIMSS) False
GSU0963 ntrC CDS None chromosome 1038168 1039571 + sigma-54 dependent DNA-binding response regulator (NCBI) True
GSU0966 GSU0966 CDS None chromosome 1040397 1040648 + hypothetical protein (VIMSS) False
GSU0967 GSU0967 CDS None chromosome 1040661 1041713 + membrane protein, putative (VIMSS) False
GSU1019 GSU1019 CDS None chromosome 1100288 1101589 + xanthine/uracil permease family protein (VIMSS) False
GSU1068 GSU1068 CDS None chromosome 1155915 1157669 - sodium/solute symporter family protein (NCBI) False
GSU1069 GSU1069 CDS None chromosome 1157898 1158206 - conserved hypothetical protein (VIMSS) False
GSU1070 GSU1070 CDS None chromosome 1158814 1160568 - sodium/solute symporter family protein (NCBI) False
GSU1071 GSU1071 CDS None chromosome 1160799 1161107 - conserved hypothetical protein (VIMSS) False
GSU1289 cheY-3 CDS None chromosome 1405494 1405859 + chemotaxis protein CheY (NCBI) False
GSU1305 gdhA CDS None chromosome 1430144 1431496 - Glu/Leu/Phe/Val dehydrogenase family protein (NCBI) False
GSU1575 GSU1575 CDS None chromosome 1726864 1727592 + hypothetical protein (VIMSS) False
GSU1762 GSU1762 CDS None chromosome 1924429 1925718 - TPR domain protein (VIMSS) False
GSU2352 GSU2352 CDS None chromosome 2572422 2574176 - sodium/solute symporter family protein (NCBI) False
GSU2353 GSU2353 CDS None chromosome 2574413 2574721 - conserved hypothetical protein (VIMSS) False
GSU2357 GSU2357 CDS None chromosome 2576714 2577760 + conserved hypothetical protein (VIMSS) False
GSU2363 GSU2363 CDS None chromosome 2589290 2591134 + chloride channel family protein, putative (VIMSS) False
GSU2462 metA CDS None chromosome 2700316 2701422 + homoserine O-acetyltransferase (NCBI) False
GSU2490 GSU2490 CDS None chromosome 2735710 2737077 + oxalate/formate antiporter, putative (VIMSS) False
GSU2706 GSU2706 CDS None chromosome 2984470 2985471 + phosphate acetyltransferase (VIMSS) False
GSU2944 GSU2944 CDS None chromosome 3241463 3242758 + (R)-2-hydroxyglutaryl-CoA dehydratase alpha-subunit, putative (VIMSS) False
GSU2945 GSU2945 CDS None chromosome 3242763 3243509 + (R)-2-hydroxyglutaryl-CoA dehydratase activator, putative (VIMSS) True
GSU2982 GSU2982 CDS None chromosome 3272590 3274689 - TonB dependent receptor, 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 32

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.