Organism : Pseudomonas aeruginosa | Module List:
Module 343 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 343

There are 28 regulatory influences for Module 343

Regulator Table (28)
Regulator Name Type
PA0034 tf
PA0514 tf
PA2838 tf
PA5344 tf
PA2005 tf
PA2510 tf
PA3045 tf
PA0893 tf
PA3381 tf
PA0906 tf
PA2846 tf
PA0748 tf
PA4659 tf
PA3458 tf
PA4341 tf
PA3711 tf
PA2681 tf
PA1998 tf
PA3678 tf
PA2050 tf
PA0564 tf
PA3714 tf
PA4989 tf
PA5337 tf
PA5293 tf
PA1374 tf
PA0701 tf
PA0515 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
3512 4.00e+01 Cctc.gaAaccTCTtatTgaa
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3513 1.10e+03 TtCATtGT
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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 343 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 5.20e-05 5.83e-04 5/22
Nitrogen metabolism kegg pathway 0.00e+00 2.00e-06 5/22
Environmental Information Processing kegg category 0.00e+00 6.00e-06 10/22
Membrane Transport kegg subcategory 8.60e-05 8.71e-04 6/22
Bacterial secretion system kegg pathway 1.00e-06 1.60e-05 5/22
Signal Transduction kegg subcategory 2.45e-04 1.84e-03 4/22
Two-component system kegg pathway 2.45e-04 1.84e-03 4/22
Microbial metabolism in diverse environments kegg pathway 4.35e-03 1.31e-02 4/22

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 5.79e-03 7.72e-03 3/22
Anaerobic tigr sub1role 0.00e+00 0.00e+00 3/22

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.10e-02 1.81e-02 8/22
Metabolism cog category 1.27e-02 2.08e-02 12/22
Cell motility cog subcategory 2.51e-03 4.56e-03 3/22
Intracellular trafficking, secretion, and vesicular transport cog subcategory 3.51e-04 7.41e-04 4/22
Energy production and conversion cog subcategory 6.32e-03 1.08e-02 4/22
Coenzyme transport and metabolism cog subcategory 5.68e-03 9.76e-03 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 343

There are 22 genes in Module 343

Gene Member Table (22)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0033 PA0033 CDS None chromosome 35905 36270 - hypothetical protein (NCBI) False
PA0034 PA0034 CDS None chromosome 36278 36901 - probable two-component response regulator (NCBI) True
PA1352 PA1352 CDS None chromosome 1466109 1467320 - hypothetical protein (NCBI) False
PA2671 PA2671 CDS None chromosome 3018848 3019927 - hypothetical protein (NCBI) False
PA2672 PA2672 CDS None chromosome 3019917 3020507 - probable type II secretion system protein (NCBI) False
PA2673 PA2673 CDS None chromosome 3020504 3020929 - probable type II secretion system protein (NCBI) False
PA2674 PA2674 CDS None chromosome 3020929 3021339 - probable type II secretion system protein (NCBI) False
PA2675 PA2675 CDS None chromosome 3021308 3021742 - probable type II secretion system protein (NCBI) False
PA2677 PA2677 CDS None chromosome 3022988 3024715 - probable type II secretion protein (NCBI) False
PA2678 PA2678 CDS None chromosome 3024705 3025508 - probable permease of ABC-2 transporter (NCBI) False
PA3870 moaA1 CDS None chromosome 4333357 4334346 - molybdopterin biosynthetic protein A1 (NCBI) False
PA3871 PA3871 CDS None chromosome 4334403 4335221 - probable peptidyl-prolyl cis-trans isomerase, PpiC-type (NCBI) False
PA3872 narI CDS None chromosome 4335276 4335959 - respiratory nitrate reductase gamma chain (NCBI) False
PA3873 narJ CDS None chromosome 4335962 4336702 - respiratory nitrate reductase delta chain (NCBI) False
PA3874 narH CDS None chromosome 4336708 4338249 - respiratory nitrate reductase beta chain (NCBI) False
PA3875 narG CDS None chromosome 4338261 4342046 - respiratory nitrate reductase alpha chain (NCBI) False
PA3876 narK2 CDS None chromosome 4342122 4343528 - nitrite extrusion protein 2 (NCBI) False
PA3877 narK1 CDS None chromosome 4343540 4344835 - nitrite extrusion protein 1 (NCBI) False
PA3914 moeA1 CDS None chromosome 4384022 4385245 - molybdenum cofactor biosynthetic protein A1 (NCBI) False
PA3915 moaB1 CDS None chromosome 4385242 4385799 - molybdopterin biosynthetic protein B1 (NCBI) False
PA5083 PA5083 CDS None chromosome 5721892 5722242 - hypothetical protein (NCBI) False
PA5084 PA5084 CDS None chromosome 5722267 5723517 - probable oxidoreductase (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 343

Please add your comments for this module by using the form below. Your comments will be publicly available.

comments powered by Disqus
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.