Organism : Pseudomonas aeruginosa | Module List:
Module 342 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 342

There are 24 regulatory influences for Module 342

Regulator Table (24)
Regulator Name Type
PA5253 tf
PA2737 tf
PA2320 tf
PA4135 tf
PA1776 tf
PA4182 tf
PA4270 tf
PA0576 tf
PA0181 tf
PA3965 tf
PA2825 tf
PA2387 tf
PA3006 tf
PA1241 tf
PA0367 tf
PA2849 tf
PA5085 tf
PA3714 tf
PA4080 tf
PA0873 tf
PA4493 tf
PA4169 tf
PA1067 tf
PA3699 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
3510 7.90e-01 TCAAacAaacttTTG.tTt
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3511 2.80e+03 gtgACcgaaAagggtc.TccgGt
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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 342 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 2.66e-03 9.47e-03 10/26
Carbohydrate Metabolism kegg subcategory 4.61e-04 3.00e-03 5/26
Glyoxylate and dicarboxylate metabolism kegg pathway 1.60e-05 2.33e-04 3/26
Butanoate metabolism kegg pathway 7.50e-05 7.86e-04 3/26
Lipid Metabolism kegg subcategory 1.78e-03 7.32e-03 3/26
Fatty acid metabolism kegg pathway 4.10e-05 4.86e-04 3/26
Amino Acid Metabolism kegg subcategory 3.12e-03 1.06e-02 5/26
Valine leucine and isoleucine degradation kegg pathway 1.35e-04 1.21e-03 3/26
Tryptophan metabolism kegg pathway 2.50e-05 3.31e-04 3/26
Metabolism of Cofactors and Vitamins kegg subcategory 5.55e-03 1.53e-02 3/26
Metabolism of Terpenoids and Polyketides kegg subcategory 1.30e-05 1.96e-04 4/26
Geraniol degradation kegg pathway 1.60e-05 2.33e-04 3/26
Xenobiotics Biodegradation and Metabolism kegg subcategory 6.00e-06 1.04e-04 5/26
Cellular Processes kegg category 3.14e-04 2.23e-03 3/26
Cell Motility kegg subcategory 3.14e-04 2.23e-03 3/26
Flagellar assembly kegg pathway 2.00e-05 2.84e-04 3/26
Global kegg category 6.94e-04 3.94e-03 10/26
Metabolism kegg subcategory 6.94e-04 3.94e-03 10/26
Metabolic pathways kegg pathway 5.33e-03 1.49e-02 8/26
Biosynthesis of secondary metabolites kegg pathway 2.79e-03 9.80e-03 5/26
Microbial metabolism in diverse environments kegg pathway 3.00e-05 3.77e-04 7/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Fatty acid and phospholipid metabolism tigr mainrole 2.00e-05 4.90e-05 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 3.32e-03 5.94e-03 15/26
Cell motility cog subcategory 5.00e-05 1.38e-04 5/26
Energy production and conversion cog subcategory 5.60e-05 1.52e-04 7/26
Lipid transport and metabolism cog subcategory 5.32e-04 1.08e-03 5/26
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 342

There are 26 genes in Module 342

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0195 pntA CDS None chromosome 224101 225219 + putative NAD(P) transhydrogenase subunit alpha 1 (NCBI) False
PA0196 pntB CDS None chromosome 225603 227039 + pyridine nucleotide transhydrogenase, beta subunit (NCBI) False
PA0482 glcB CDS None chromosome 542170 544347 - malate synthase (NCBI) False
PA0506 PA0506 CDS None chromosome 564914 566719 + probable acyl-CoA dehydrogenase (NCBI) False
PA1092 fliC CDS None chromosome 1183058 1184524 + flagellin type B (NCBI) False
PA1093 PA1093 CDS None chromosome 1184603 1184974 + hypothetical protein (NCBI) False
PA1094 fliD CDS None chromosome 1185060 1186484 + flagellar capping protein FliD (NCBI) False
PA1095 PA1095 CDS None chromosome 1186606 1186986 + flagellar protein FliS (NCBI) False
PA1096 PA1096 CDS None chromosome 1187009 1187305 + hypothetical protein (NCBI) False
PA1244 PA1244 CDS None chromosome 1348060 1348401 - hypothetical protein (NCBI) False
PA1772 PA1772 CDS None chromosome 1917599 1918087 + ribonuclease activity regulator protein RraA (NCBI) False
PA1830 PA1830 CDS None chromosome 1989109 1989423 - hypothetical protein (NCBI) False
PA2634 PA2634 CDS None chromosome 2977756 2979351 + isocitrate lyase (NCBI) False
PA2951 etfA CDS None chromosome 3310792 3311721 - electron transfer flavoprotein alpha-subunit (NCBI) False
PA2952 etfB CDS None chromosome 3311721 3312470 - electron transfer flavoprotein beta-subunit (NCBI) False
PA2953 PA2953 CDS None chromosome 3312791 3314446 + electron transfer flavoprotein-ubiquinone oxidoreductase (NCBI) False
PA3013 foaB CDS None chromosome 3373254 3374429 - acetyl-CoA acetyltransferase (NCBI) False
PA3014 faoA CDS None chromosome 3374460 3376607 - fatty-acid oxidation complex alpha-subunit (NCBI) False
PA3203 PA3203 CDS None chromosome 3594208 3594570 + hypothetical protein (NCBI) False
PA3204 PA3204 CDS None chromosome 3594581 3595258 + probable two-component response regulator (NCBI) False
PA3205 PA3205 CDS None chromosome 3595387 3595827 + hypothetical protein (NCBI) False
PA3925 PA3925 CDS None chromosome 4400123 4401298 + probable acyl-CoA thiolase (NCBI) False
PA4163 PA4163 CDS None chromosome 4658450 4660159 + amidase (NCBI) False
PA4164 PA4164 CDS None chromosome 4660221 4660547 + hypothetical protein (NCBI) False
PA4176 ppiC2 CDS None chromosome 4673038 4673319 - peptidyl-prolyl cis-trans isomerase C2 (NCBI) False
PA4180 PA4180 CDS None chromosome 4676282 4677925 - hypothetical protein (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.

Comments for Module 342

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.