Organism : Pseudomonas aeruginosa | Module List:
Module 229 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 229

There are 17 regulatory influences for Module 229

Regulator Table (17)
Regulator Name Type
PA3604 tf
PA1141 tf
PA2115 tf
PA2859 tf
PA0037 tf
PA1285 tf
PA3322 tf
PA1359 tf
PA1184 tf
PA4769 tf
PA2802 tf
PA0828 tf
PA4145 tf
PA3266 tf
PA0514 tf
PA1853 tf
PA2020 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
3286 1.50e+02 CgGgTAGAATgccCGcC.cTc
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3287 1.00e+03 agGc.gtACactGgGCg
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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 229 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 2.47e-02 3.87e-02 11/35
Coenzyme transport and metabolism cog subcategory 2.90e-02 4.49e-02 3/35
Function unknown cog subcategory 2.75e-02 4.27e-02 6/35
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 229

There are 35 genes in Module 229

Gene Member Table (35)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0419 PA0419 CDS None chromosome 466018 466740 - hypothetical protein (NCBI) False
PA0560 PA0560 CDS None chromosome 617662 618150 + hypothetical protein (NCBI) False
PA0948 PA0948 CDS None chromosome 1036158 1036577 - hypothetical protein (NCBI) False
PA0951 PA0951 CDS None chromosome 1037650 1038885 + probable ribonuclease (NCBI) False
PA0995 ogt CDS None chromosome 1077383 1077904 - methylated-DNA--protein-cysteinemethyltransferase (NCBI) False
PA1075 PA1075 CDS None chromosome 1163276 1163593 + hypothetical protein (NCBI) False
PA1139 PA1139 CDS None chromosome 1230310 1231158 + hypothetical protein (NCBI) False
PA1141 PA1141 CDS None chromosome 1232229 1233131 - probable transcriptional regulator (NCBI) True
PA1222 PA1222 CDS None chromosome 1324793 1325950 - probable membrane-bound lytic murein transglycolase A (NCBI) False
PA1285 PA1285 CDS None chromosome 1396731 1397180 + probable transcriptional regulator (NCBI) True
PA1398 PA1398 CDS None chromosome 1519627 1519968 + hypothetical protein (NCBI) False
PA1594 PA1594 CDS None chromosome 1735706 1736152 + hypothetical protein (NCBI) False
PA1645 PA1645 CDS None chromosome 1790472 1790879 - hypothetical protein (NCBI) False
PA1686 alkA CDS None chromosome 1835325 1836218 - DNA-3-methyladenine glycosidase II (NCBI) False
PA2568 PA2568 CDS None chromosome 2904040 2904447 - hypothetical protein (NCBI) False
PA2695 PA2695 CDS None chromosome 3048051 3049154 - hypothetical protein (NCBI) False
PA2773 PA2773 CDS None chromosome 3131509 3132030 - hypothetical protein (NCBI) False
PA2860 PA2860 CDS None chromosome 3213044 3213484 - hypothetical protein (NCBI) False
PA3130 PA3130 CDS None chromosome 3511957 3512394 - hypothetical protein (NCBI) False
PA3131 PA3131 CDS None chromosome 3512394 3513041 - probable aldolase (NCBI) False
PA3178 PA3178 CDS None chromosome 3568636 3569013 - hypothetical protein (NCBI) False
PA3288 PA3288 CDS None chromosome 3680465 3680968 - hypothetical protein (NCBI) False
PA3463 PA3463 CDS None chromosome 3873606 3873836 + hypothetical protein (NCBI) False
PA3958 PA3958 CDS None chromosome 4437390 4438529 + hypothetical protein (NCBI) False
PA3968 PA3968 CDS None chromosome 4446425 4446994 - probable pseudouridine synthase (NCBI) False
PA4075 PA4075 CDS None chromosome 4553524 4554360 - hypothetical protein (NCBI) False
PA4637 PA4637 CDS None chromosome 5206209 5206487 - hypothetical protein (NCBI) False
PA4718 PA4718 CDS None chromosome 5297007 5297483 - hypothetical protein (NCBI) False
PA4783 PA4783 CDS None chromosome 5370755 5371645 - hypothetical protein (NCBI) False
PA4789 PA4789 CDS None chromosome 5377791 5378096 + hypothetical protein (NCBI) False
PA4790 PA4790 CDS None chromosome 5378093 5378842 + hypothetical protein (NCBI) False
PA5019 PA5019 CDS None chromosome 5644454 5645290 - hypothetical protein (NCBI) False
PA5228 PA5228 CDS None chromosome 5884508 5885119 + hypothetical protein (NCBI) False
PA5259 hemD CDS None chromosome 5920742 5921497 - uroporphyrinogen-III synthetase (NCBI) False
PA5485 PA5485 CDS None chromosome 6176516 6177295 - 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.