Organism : Pseudomonas aeruginosa | Module List:
Module 104 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 104

There are 16 regulatory influences for Module 104

Regulator Table (16)
Regulator Name Type
PA3381 tf
PA2838 tf
PA1196 tf
PA3364 tf
PA2586 tf
PA3921 tf
PA4769 tf
PA4914 tf
PA4745 tf
PA4341 tf
PA3574 tf
PA2696 tf
PA3594 tf
PA5288 tf
PA1153 tf
PA1097 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
3040 2.10e-11 aACAAgAAac
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3041 7.60e+03 AcCacgActTtCcgTTgCA.t
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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 104 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Xenobiotics Biodegradation and Metabolism kegg subcategory 1.17e-04 1.08e-03 4/27
Benzoate degradation kegg pathway 5.80e-05 6.38e-04 3/27
Fluorobenzoate degradation kegg pathway 0.00e+00 1.00e-06 3/27
Environmental Information Processing kegg category 4.03e-03 1.24e-02 6/27
Signal Transduction kegg subcategory 5.55e-03 1.53e-02 3/27
Two-component system kegg pathway 5.55e-03 1.53e-02 3/27
Microbial metabolism in diverse environments kegg pathway 1.08e-02 2.43e-02 4/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 1.88e-02 2.18e-02 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Carbohydrate transport and metabolism cog subcategory 1.55e-02 2.51e-02 3/27
Lipid transport and metabolism cog subcategory 2.35e-02 3.70e-02 3/27
Secondary metabolites biosynthesis, transport and catabolism cog subcategory 1.00e-06 3.00e-06 7/27
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 104

There are 27 genes in Module 104

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0229 pcaT CDS None chromosome 258463 259761 + dicarboxylic acid transporter PcaT (NCBI) False
PA0695 PA0695 CDS None chromosome 767601 768347 + hypothetical protein (NCBI) False
PA0697 PA0697 CDS None chromosome 770156 770818 + hypothetical protein (NCBI) False
PA0699 PA0699 CDS None chromosome 771331 772275 + probable peptidyl-prolyl cis-trans isomerase, PpiC-type (NCBI) False
PA0751 PA0751 CDS None chromosome 818825 819862 - hypothetical protein (NCBI) False
PA0752 PA0752 CDS None chromosome 819855 821372 - hypothetical protein (NCBI) False
PA0753 PA0753 CDS None chromosome 821383 821853 - hypothetical protein (NCBI) False
PA0754 PA0754 CDS None chromosome 821902 822885 - hypothetical protein (NCBI) False
PA0755 PA0755 CDS None chromosome 822915 824198 - probable porin (NCBI) False
PA1153 PA1153 CDS None chromosome 1247932 1248486 - hypothetical protein (NCBI) True
PA1169 PA1169 CDS None chromosome 1267680 1269737 + probable lipoxygenase (NCBI) False
PA1409 aphA CDS None chromosome 1533238 1534278 + acetylpolyamine aminohydrolase (NCBI) False
PA1410 PA1410 CDS None chromosome 1534289 1535380 + probable periplasmic spermidine/putrescine-binding protein (NCBI) False
PA2003 bdhA CDS None chromosome 2190084 2190854 - 3-hydroxybutyrate dehydrogenase (NCBI) False
PA2004 PA2004 CDS None chromosome 2190891 2192282 - hypothetical protein (NCBI) False
PA2341 PA2341 CDS None chromosome 2585299 2586411 + probable ATP-binding component of ABC maltose/mannitol transporter (NCBI) False
PA2507 catA CDS None chromosome 2824659 2825591 - catechol 1,2-dioxygenase (NCBI) False
PA2508 catC CDS None chromosome 2825636 2825926 - muconolactone delta-isomerase (NCBI) False
PA2515 xylL CDS None chromosome 2832369 2833130 - cis-1,2-dihydroxycyclohexa-3,4-diene carboxylate dehydrogenase (NCBI) False
PA2525 PA2525 CDS None chromosome 2846283 2847779 - probable outer membrane protein precursor (NCBI) False
PA2682 PA2682 CDS None chromosome 3029187 3030428 + hypothetical protein (NCBI) False
PA3669 PA3669 CDS None chromosome 4107505 4108485 - hypothetical protein (NCBI) False
PA3670 PA3670 CDS None chromosome 4108489 4110336 - hypothetical protein (NCBI) False
PA3671 PA3671 CDS None chromosome 4110347 4111081 - probable permease of ABC transporter (NCBI) False
PA3860 PA3860 CDS None chromosome 4318922 4320820 - acyl-CoA synthase (NCBI) False
PA5265 PA5265 CDS None chromosome 5927336 5930605 - hypothetical protein (NCBI) False
PA5266 PA5266 CDS None chromosome 5930602 5932677 - 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 104

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.