Organism : Pseudomonas aeruginosa | Module List:
Module 239 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 239

There are 40 regulatory influences for Module 239

Regulator Table (40)
Regulator Name Type
PA5380 tf
PA1759 tf
PA1159 tf
PA1760 tf
PA4436 tf
PA0708 tf
PA2376 tf
PA4755 tf
PA5337 tf
PA1949 tf
PA1853 tf
PA0784 tf
PA4853 tf
PA0652 tf
PA4659 tf
PA0533 tf
PA5288 tf
PA1713 tf
PA2332 tf
PA1285 tf
PA4769 tf
PA0367 tf
PA1015 tf
PA2577 tf
PA2020 tf
PA2267 tf
PA2010 tf
PA1978 tf
PA3215 tf
PA0797 tf
PA2713 tf
PA0424 tf
PA1099 tf
PA4787 tf
PA2917 tf
PA4185 tf
PA3249 tf
PA3771 tf
PA2016 tf
PA0764 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
3306 5.60e-21 cacaAtAAcaAtaA.aa
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3307 2.50e+02 AgacctctgTtatttta.CGtgA
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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 239 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 1.65e-02 3.33e-02 3/25
Glycolysis / Gluconeogenesis kegg pathway 1.70e-05 2.48e-04 3/25
Pyruvate metabolism kegg pathway 8.70e-05 8.83e-04 3/25
Propanoate metabolism kegg pathway 7.50e-05 7.84e-04 3/25
Lipid Metabolism kegg subcategory 1.53e-03 6.63e-03 3/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 1.44e-02 1.71e-02 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.80e-05 6.20e-05 18/25
Carbohydrate transport and metabolism cog subcategory 2.14e-04 4.75e-04 5/25
Amino acid transport and metabolism cog subcategory 9.52e-04 1.85e-03 7/25
Lipid transport and metabolism cog subcategory 3.09e-03 5.56e-03 4/25
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 239

There are 25 genes in Module 239

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0129 gabP CDS None chromosome 145965 147392 - gamma-aminobutyrate permease (NCBI) False
PA0866 aroP2 CDS None chromosome 947205 948623 + aromatic amino acid transport protein AroP2 (NCBI) False
PA0887 acsA CDS None chromosome 969670 971625 + acetyl-coenzyme A synthetase (NCBI) False
PA1759 PA1759 CDS None chromosome 1898816 1901521 + probable transcriptional regulator (NCBI) True
PA1760 PA1760 CDS None chromosome 1901524 1904247 + probable transcriptional regulator (NCBI) True
PA1984 PA1984 CDS None chromosome 2169988 2171508 + probable aldehyde dehydrogenase (NCBI) False
PA1991 PA1991 CDS None chromosome 2176974 2178137 + probable iron-containing alcohol dehydrogenase (NCBI) False
PA2002 PA2002 CDS None chromosome 2188459 2189883 + hypothetical protein (NCBI) False
PA2006 PA2006 CDS None chromosome 2194058 2195410 - probable major facilitator superfamily (MFS) transporter (NCBI) False
PA2557 PA2557 CDS None chromosome 2890356 2892050 - acyl-CoA synthase (NCBI) False
PA3038 PA3038 CDS None chromosome 3400684 3401949 + probable porin (NCBI) False
PA3186 oprB CDS None chromosome 3575912 3577276 - Glucose/carbohydrate outer membrane porin OprB precursor (NCBI) False
PA3187 PA3187 CDS None chromosome 3577320 3578480 - probable ATP-binding component of ABC transporter (NCBI) False
PA3188 PA3188 CDS None chromosome 3578513 3579358 - probable permease of ABC sugar transporter (NCBI) False
PA3189 PA3189 CDS None chromosome 3579351 3580283 - probable permease of ABC sugar transporter (NCBI) False
PA3190 PA3190 CDS None chromosome 3580384 3581646 - probable binding protein component of ABC sugar transporter (NCBI) False
PA3234 actP CDS None chromosome 3621505 3623160 - acetate permease (NCBI) False
PA3235 PA3235 CDS None chromosome 3623157 3623468 - hypothetical protein (NCBI) False
PA3710 PA3710 CDS None chromosome 4154339 4156012 - probable GMC-type oxidoreductase (NCBI) False
PA4023 PA4023 CDS None chromosome 4504001 4505449 + probable transport protein (NCBI) False
PA4024 eutB CDS None chromosome 4505508 4506902 + ethanolamine ammonia-lyase large subunit (NCBI) False
PA4025 PA4025 CDS None chromosome 4506913 4507734 + ethanolamine ammonia-lyase small subunit (NCBI) False
PA4733 acsB CDS None chromosome 5315534 5317471 + acetyl-coenzyme A synthetase (NCBI) False
PA5153 PA5153 CDS None chromosome 5801315 5802067 + probable periplasmic binding protein (NCBI) False
PA5380 PA5380 CDS None chromosome 6058673 6059776 + probable transcriptional regulator (NCBI) True

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.