Organism : Pseudomonas aeruginosa | Module List:
Module 187 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 187

There are 10 regulatory influences for Module 187

Regulator Table (10)
Regulator Name Type
PA2115 tf
PA1403 tf
PA0218 tf
PA3898 tf
PA3594 tf
PA1850 tf
PA2758 tf
PA3269 tf
PA0828 tf
PA3565 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
3202 6.40e+02 TCgagC.cctcg.ccagGcccTc
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3203 1.90e+02 g.CggCagCgcCcGcgCgacg
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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 187 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 1.95e-02 3.11e-02 11/34
Coenzyme transport and metabolism cog subcategory 2.63e-02 4.11e-02 3/34
General function prediction only cog subcategory 2.18e-02 3.44e-02 7/34
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 187

There are 34 genes in Module 187

Gene Member Table (34)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0048 PA0048 CDS None chromosome 62403 62786 - probable transcriptional regulator (NCBI) False
PA0433 PA0433 CDS None chromosome 484404 484838 + hypothetical protein (NCBI) False
PA0801 PA0801 CDS None chromosome 879557 881077 + hypothetical protein (NCBI) False
PA0849 trxB2 CDS None chromosome 927880 928830 + thioredoxin reductase 2 (NCBI) False
PA1139 PA1139 CDS None chromosome 1230310 1231158 + hypothetical protein (NCBI) False
PA1140 PA1140 CDS None chromosome 1231256 1232092 - hypothetical protein (NCBI) False
PA1331 PA1331 CDS None chromosome 1442904 1444451 - hypothetical protein (NCBI) False
PA1403 PA1403 CDS None chromosome 1525667 1526299 + probable transcriptional regulator (NCBI) True
PA1472 PA1472 CDS None chromosome 1599428 1599982 - hypothetical protein (NCBI) False
PA1870 PA1870 CDS None chromosome 2031988 2032413 + hypothetical protein (NCBI) False
PA1966 PA1966 CDS None chromosome 2149472 2149843 + hypothetical protein (NCBI) False
PA2115 PA2115 CDS None chromosome 2326334 2327287 + probable transcriptional regulator (NCBI) True
PA2170 PA2170 CDS None chromosome 2393424 2393633 + hypothetical protein (NCBI) False
PA2184 PA2184 CDS None chromosome 2405230 2405739 - hypothetical protein (NCBI) False
PA2650 PA2650 CDS None chromosome 2997840 2998649 + hypothetical protein (NCBI) False
PA2694 PA2694 CDS None chromosome 3047644 3047970 - probable thioredoxin (NCBI) False
PA3030 mobA CDS None chromosome 3394088 3394684 + molybdopterin-guanine dinucleotide biosynthesis protein A (NCBI) False
PA3196 PA3196 CDS None chromosome 3588741 3589271 - hypothetical protein (NCBI) False
PA3269 PA3269 CDS None chromosome 3658248 3659102 - probable transcriptional regulator (NCBI) True
PA3271 PA3271 CDS None chromosome 3660022 3663501 + probable two-component sensor (NCBI) False
PA3436 PA3436 CDS None chromosome 3844385 3844942 + hypothetical protein (NCBI) False
PA3883 PA3883 CDS None chromosome 4349502 4350332 + short chain dehydrogenase (NCBI) False
PA3886 PA3886 CDS None chromosome 4351595 4352494 + hypothetical protein (NCBI) False
PA3898 PA3898 CDS None chromosome 4366301 4367182 + probable transcriptional regulator (NCBI) True
PA3957 PA3957 CDS None chromosome 4436492 4437328 - short chain dehydrogenase (NCBI) False
PA4183 PA4183 CDS None chromosome 4679599 4680066 - hypothetical protein (NCBI) False
PA4290 PA4290 CDS None chromosome 4812598 4814214 - probable chemotaxis transducer (NCBI) False
PA4361 PA4361 CDS None chromosome 4889112 4890101 - probable oxidoreductase (NCBI) False
PA4626 hprA CDS None chromosome 5193196 5194167 + glycerate dehydrogenase (NCBI) False
PA4631 PA4631 CDS None chromosome 5198334 5199359 - hypothetical protein (NCBI) False
PA5073 PA5073 CDS None chromosome 5711008 5711469 + hypothetical protein (NCBI) False
PA5123 PA5123 CDS None chromosome 5771455 5772027 + hypothetical protein (NCBI) False
PA5314 PA5314 CDS None chromosome 5985219 5985581 + hypothetical protein (NCBI) False
PA5533 PA5533 CDS None chromosome 6227082 6227450 + 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.

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.