Organism : Pseudomonas aeruginosa | Module List:
Module 192 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 192

There are 16 regulatory influences for Module 192

Regulator Table (16)
Regulator Name Type
PA3711 tf
PA5032 tf
PA3420 tf
PA1312 tf
PA1138 tf
PA5218 tf
PA2032 tf
PA3830 tf
PA4288 tf
PA5525 tf
PA5293 tf
PA1380 tf
PA4363 tf
PA5431 tf
PA1261 tf
PA3630 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
3212 1.40e-03 AtAcgTcTgTattcatattg
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3213 3.90e-01 TAtGaAAAAgGAAT
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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 192 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Lipid Metabolism kegg subcategory 2.69e-04 1.99e-03 4/29
Xenobiotics Biodegradation and Metabolism kegg subcategory 1.86e-03 7.49e-03 3/29
Microbial metabolism in diverse environments kegg pathway 1.46e-02 3.04e-02 4/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 4.29e-03 7.54e-03 9/29
Transcription cog subcategory 4.47e-04 9.23e-04 8/29
Lipid transport and metabolism cog subcategory 6.05e-03 1.04e-02 4/29
Transcriptional regulator cog 2.00e-06 1.00e-05 6/29
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 192

There are 29 genes in Module 192

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0142 PA0142 CDS None chromosome 161906 163255 + hydroxydechloroatrazine ethylaminohydrolase (NCBI) False
PA0347 glpQ CDS None chromosome 389733 390884 - glycerophosphoryl diester phosphodiesterase, periplasmic (NCBI) False
PA0676 PA0676 CDS None chromosome 735487 736446 + probable transmembrane sensor (NCBI) False
PA1138 PA1138 CDS None chromosome 1229344 1230219 + probable transcriptional regulator (NCBI) True
PA1264 PA1264 CDS None chromosome 1372979 1373845 - probable transcriptional regulator (NCBI) True
PA1282 PA1282 CDS None chromosome 1392564 1394069 - probable major facilitator superfamily (MFS) transporter (NCBI) False
PA1312 PA1312 CDS None chromosome 1422355 1423266 - probable transcriptional regulator (NCBI) True
PA1345 PA1345 CDS None chromosome 1458707 1460296 + hypothetical protein (NCBI) False
PA1503 PA1503 CDS None chromosome 1633006 1633437 + hypothetical protein (NCBI) False
PA1628 PA1628 CDS None chromosome 1771122 1772651 - probable 3-hydroxyacyl-CoA dehydrogenase (NCBI) False
PA1635 kdpC CDS None chromosome 1779877 1780428 + potassium-transporting ATPase subunit C (NCBI) False
PA2032 PA2032 CDS None chromosome 2221337 2222761 + probable transcriptional regulator (NCBI) True
PA2574 alkB1 CDS None chromosome 2910729 2911877 - alkane-1-monooxygenase (NCBI) False
PA3387 rhlG CDS None chromosome 3792290 3793060 + beta-ketoacyl reductase (NCBI) False
PA3464 PA3464 CDS None chromosome 3874654 3875979 - hypothetical protein (NCBI) False
PA3711 PA3711 CDS None chromosome 4156184 4157089 + probable transcriptional regulator (NCBI) True
PA3718 PA3718 CDS None chromosome 4164330 4165571 - probable major facilitator superfamily (MFS) transporter (NCBI) False
PA3733 PA3733 CDS None chromosome 4183710 4184939 + hypothetical protein (NCBI) False
PA4038 PA4038 CDS None chromosome 4520198 4520932 + hypothetical protein (NCBI) False
PA4082 cupB5 CDS None chromosome 4561540 4564596 - adhesive protein CupB5 (NCBI) False
PA4092 hpaC CDS None chromosome 4575332 4575844 + 4-hydroxyphenylacetate 3-monooxygenase small chain (NCBI) False
PA4287 PA4287 CDS None chromosome 4809547 4810437 - hypothetical protein (NCBI) False
PA4288 PA4288 CDS None chromosome 4810538 4811341 + probable transcriptional regulator (NCBI) True
PA4330 PA4330 CDS None chromosome 4858490 4859263 - probable enoyl-CoA hydratase/isomerase (NCBI) False
PA4351 PA4351 CDS None chromosome 4879545 4880321 + probable acyltransferase (NCBI) False
PA4363 iciA CDS None chromosome 4891345 4892247 - chromosome replication initiation inhibitor protein (NCBI) True
PA4586 PA4586 CDS None chromosome 5135816 5136193 + hypothetical protein (NCBI) False
PA5218 PA5218 CDS None chromosome 5875653 5876567 - probable transcriptional regulator (NCBI) True
PA5381 PA5381 CDS None chromosome 6059823 6060200 - 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 192

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.