Organism : Geobacter sulfurreducens | Module List:
Module 64 Profile

GeneModule member RegulatorRegulator MotifMotif
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 64

There are 15 regulatory influences for Module 64

Regulator Table (15)
Regulator Name Type
GSU0164 tf
GSU0812 tf
GSU1483 tf
GSU2237 tf
GSU1542 tf
GSU0191 tf
GSU1382 tf
GSU2987 tf
GSU0366 tf
GSU3109 tf
GSU0254 tf
GSU3127 tf
GSU1653 tf
GSU1270 tf
GSU2809 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
2288 2.30e-02 gg.g.CtTttccttTgccggcAA
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2289 6.80e+02 TgCGT.AAgg
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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 64 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.40e-02 3.34e-02 7/22
Energy Metabolism kegg subcategory 1.00e-06 3.80e-05 7/22
Nitrogen metabolism kegg pathway 0.00e+00 0.00e+00 7/22
Xenobiotics Biodegradation and Metabolism kegg subcategory 0.00e+00 2.20e-05 3/22
Chloroalkane and chloroalkene degradation kegg pathway 0.00e+00 0.00e+00 3/22
Microbial metabolism in diverse environments kegg pathway 4.63e-03 1.67e-02 3/22

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Central intermediary metabolism tigr mainrole 0.00e+00 0.00e+00 7/22
Nitrogen fixation tigr sub1role 0.00e+00 0.00e+00 7/22
Transport and binding proteins tigr mainrole 1.11e-03 2.14e-03 3/22

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 9.62e-03 1.74e-02 10/22
Inorganic ion transport and metabolism cog subcategory 1.46e-04 3.54e-04 5/22
Nitrogenase molybdenum-iron protein, alpha and beta chains cog 0.00e+00 0.00e+00 3/22
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 64

There are 22 genes in Module 64

Gene Member Table (22)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
GSU0868 GSU0868 CDS None chromosome 924358 925770 + conserved hypothetical protein TIGR00159 (NCBI) False
GSU0937 nifV CDS None chromosome 1007092 1008243 + homocitrate synthase (NCBI) False
GSU0938 GSU0938 CDS None chromosome 1008591 1009343 + hypothetical protein (VIMSS) False
GSU0939 GSU0939 CDS None chromosome 1009395 1009733 + nitrogen regulatory protein P-II, putative (VIMSS) False
GSU0940 GSU0940 CDS None chromosome 1009771 1011240 + ammonium transporter (VIMSS) False
GSU0941 GSU0941 CDS None chromosome 1011471 1012217 + sensor histidine kinase, putative (VIMSS) False
GSU0968 GSU0968 CDS None chromosome 1041859 1043229 + hypothetical protein (VIMSS) False
GSU1221 GSU1221 CDS None chromosome 1324618 1325838 - ammonium transporter, putative (VIMSS) False
GSU2798 GSU2798 CDS None chromosome 3077578 3078381 - acetyltransferase, GNAT family (NCBI) False
GSU2799 GSU2799 CDS None chromosome 3078386 3079258 - radical SAM domain protein (NCBI) False
GSU2802 dRAT CDS None chromosome 3082277 3083074 - NAD(+)--dinitrogen-reductase ADP-D-ribosyltransferase (NCBI) False
GSU2803 GSU2803 CDS None chromosome 3083133 3083462 - dinitrogenase iron-molybdenum cofactor family protein (NCBI) False
GSU2804 GSU2804 CDS None chromosome 3083491 3083754 - ferredoxin family protein (VIMSS) False
GSU2805 nifX CDS None chromosome 3083822 3084211 - nitrogenase molybdenum-iron cofactor biosynthesis protein NifX (NCBI) False
GSU2806 nifEN CDS None chromosome 3084293 3087052 - nitrogenase molybdenum-iron cofactor biosynthesis protein NifEN (NCBI) False
GSU2819 nifK CDS None chromosome 3100763 3102232 - nitrogenase molybdenum-iron protein, beta subunit (NCBI) False
GSU2820 nifD CDS None chromosome 3102400 3103839 - nitrogenase molybdenum-iron protein, alpha chain (NCBI) False
GSU2821 nifH CDS None chromosome 3104018 3104887 - nitrogenase iron protein (VIMSS) False
GSU2822 GSU2822 CDS None chromosome 3105261 3105836 - response regulator (VIMSS) False
GSU2961 modB CDS None chromosome 3257691 3258374 - molybdenum ABC transporter, permease protein modB (NCBI) False
GSU2962 modA CDS None chromosome 3258378 3259130 - molybdenum ABC transporter, periplasmic molybdenum-binding protein modA (NCBI) False
GSU3143 GSU3143 CDS None chromosome 3451151 3451585 + peptidyl-prolyl cis-trans isomerase, FKBP-type, putative (NCBI) 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.

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.