Organism : Pseudomonas aeruginosa | Module List:
Module 245 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 245

There are 23 regulatory influences for Module 245

Regulator Table (23)
Regulator Name Type
PA4984 tf
PA4203 tf
PA0873 tf
PA3711 tf
PA5253 tf
PA1359 tf
PA3782 tf
PA0780 tf
PA4764 tf
PA1309 tf
PA3220 tf
PA1607 tf
PA4989 tf
PA3594 tf
PA2020 tf
PA3508 tf
PA3830 tf
PA2032 tf
PA4906 tf
PA3604 tf
PA1335 tf
PA2885 tf
PA2957 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
3318 3.30e+03 gCttTTCC
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3319 3.30e+04 GAAATcCAt
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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 245 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 1.03e-02 1.70e-02 13/39
Signal transduction mechanisms cog subcategory 2.38e-02 3.74e-02 5/39
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 245

There are 39 genes in Module 245

Gene Member Table (39)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0255 PA0255 CDS None chromosome 286338 287024 - hypothetical protein (NCBI) False
PA0307 PA0307 CDS None chromosome 348440 349051 - hypothetical protein (NCBI) False
PA0360 PA0360 CDS None chromosome 403295 404281 + hypothetical protein (NCBI) False
PA0584 cca CDS None chromosome 641932 643164 - tRNA nucleotidyl transferase (NCBI) False
PA0600 PA0600 CDS None chromosome 660315 662708 + probable two-component sensor (NCBI) False
PA0780 pruR CDS None chromosome 848383 849135 + proline utilization regulator (NCBI) True
PA0787 PA0787 CDS None chromosome 859007 860170 + hypothetical protein (NCBI) False
PA1242 PA1242 CDS None chromosome 1343453 1345225 + hypothetical protein (NCBI) False
PA1325 PA1325 CDS None chromosome 1436663 1437070 + hypothetical protein (NCBI) False
PA1451 PA1451 CDS None chromosome 1578839 1580182 + hypothetical protein (NCBI) False
PA1469 PA1469 CDS None chromosome 1597365 1598087 + hypothetical protein (NCBI) False
PA1576 PA1576 CDS None chromosome 1715809 1716675 + probable 3-hydroxyisobutyrate dehydrogenase (NCBI) False
PA1672 PA1672 CDS None chromosome 1824343 1824723 - hypothetical protein (NCBI) False
PA1841 PA1841 CDS None chromosome 1998963 1999460 + hypothetical protein (NCBI) False
PA1960 PA1960 CDS None chromosome 2144077 2144799 + hypothetical protein (NCBI) False
PA2032 PA2032 CDS None chromosome 2221337 2222761 + probable transcriptional regulator (NCBI) True
PA2558 PA2558 CDS None chromosome 2892271 2892963 + probable transport protein (NCBI) False
PA2695 PA2695 CDS None chromosome 3048051 3049154 - hypothetical protein (NCBI) False
PA2712 PA2712 CDS None chromosome 3066296 3067159 + hypothetical protein (NCBI) False
PA2842 PA2842 CDS None chromosome 3196717 3197466 - hypothetical protein (NCBI) False
PA2860 PA2860 CDS None chromosome 3213044 3213484 - hypothetical protein (NCBI) False
PA3015 PA3015 CDS None chromosome 3377035 3377853 + hypothetical protein (NCBI) False
PA3178 PA3178 CDS None chromosome 3568636 3569013 - hypothetical protein (NCBI) False
PA3782 PA3782 CDS None chromosome 4241342 4242295 - probable transcriptional regulator (NCBI) True
PA3825 PA3825 CDS None chromosome 4282078 4283658 - hypothetical protein (NCBI) False
PA4114 PA4114 CDS None chromosome 4601574 4602083 - spermidine acetyltransferase (NCBI) False
PA4374 PA4374 CDS None chromosome 4903466 4904596 + probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) False
PA4383 PA4383 CDS None chromosome 4914127 4914510 - hypothetical protein (NCBI) False
PA4531 PA4531 CDS None chromosome 5074409 5074618 - hypothetical protein (NCBI) False
PA4656 PA4656 CDS None chromosome 5223559 5224476 - hypothetical protein (NCBI) False
PA4716 PA4716 CDS None chromosome 5295170 5296024 + hypothetical protein (NCBI) False
PA4780 PA4780 CDS None chromosome 5368170 5369063 - hypothetical protein (NCBI) False
PA4983 PA4983 CDS None chromosome 5598308 5599042 - probable two-component response regulator (NCBI) False
PA4984 PA4984 CDS None chromosome 5599160 5599807 - probable transcriptional regulator (NCBI) True
PA5145 PA5145 CDS None chromosome 5792505 5793611 + hypothetical protein (NCBI) False
PA5200 ompR CDS None chromosome 5852653 5853396 - two-component response regulator OmpR (NCBI) False
PA5248 PA5248 CDS None chromosome 5908397 5910298 - hypothetical protein (NCBI) False
PA5275 cyaY CDS None chromosome 5940747 5941082 - frataxin-like protein (NCBI) False
PA5287 amtB CDS None chromosome 5951115 5952443 - ammonium transporter AmtB (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 245

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.