Organism : Pseudomonas aeruginosa | Module List:
Module 125 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 125

There are 18 regulatory influences for Module 125

Regulator Table (18)
Regulator Name Type
PA4600 tf
PA0491 tf
PA3594 tf
PA0191 tf
PA1430 tf
PA3711 tf
PA4989 tf
PA5344 tf
PA0120 tf
PA1223 tf
PA2802 tf
PA4363 tf
PA1235 tf
PA1003 tf
PA3381 tf
PA0268 tf
PA5293 tf
PA1520 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
3080 1.00e-10 ataagatcAttctAgaCAATa
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3081 1.10e-07 ACAAcaAgAaAgatg
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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 125 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 2.52e-03 9.22e-03 5/25
Xenobiotics Biodegradation and Metabolism kegg subcategory 1.05e-03 5.12e-03 3/25
Global kegg category 2.47e-02 4.54e-02 7/25
Metabolism kegg subcategory 2.47e-02 4.54e-02 7/25
Biosynthesis of secondary metabolites kegg pathway 1.19e-02 2.59e-02 4/25
Microbial metabolism in diverse environments kegg pathway 1.32e-03 5.98e-03 5/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 2.30e-03 3.44e-03 4/25
Unknown substrate tigr sub1role 9.00e-06 2.60e-05 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.85e-03 3.45e-03 15/25
Cell wall/membrane/envelope biogenesis cog subcategory 2.26e-02 3.56e-02 3/25
Energy production and conversion cog subcategory 1.11e-02 1.83e-02 4/25
Amino acid transport and metabolism cog subcategory 4.61e-03 8.06e-03 6/25
Lipid transport and metabolism cog subcategory 1.81e-02 2.89e-02 3/25
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 125

There are 25 genes in Module 125

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0119 PA0119 CDS None chromosome 138818 140167 + probable dicarboxylate transporter (NCBI) False
PA0120 PA0120 CDS None chromosome 140216 140902 + probable transcriptional regulator (NCBI) True
PA0491 PA0491 CDS None chromosome 550867 551793 - probable transcriptional regulator (NCBI) True
PA0492 PA0492 CDS None chromosome 551911 552669 + hypothetical protein (NCBI) False
PA0493 PA0493 CDS None chromosome 552746 552994 + acetyl-CoA carboxylase (NCBI) False
PA0494 PA0494 CDS None chromosome 553005 554381 + acetyl-CoA carboxylase (NCBI) False
PA0495 PA0495 CDS None chromosome 554383 555261 + hypothetical protein (NCBI) False
PA0496 PA0496 CDS None chromosome 555251 556228 + hypothetical protein (NCBI) False
PA2845 PA2845 CDS None chromosome 3200320 3200553 - hypothetical protein (NCBI) False
PA4073 PA4073 CDS None chromosome 4551143 4552630 - probable aldehyde dehydrogenase (NCBI) False
PA4100 PA4100 CDS None chromosome 4582852 4584531 + probable dehydrogenase (NCBI) False
PA4185 PA4185 CDS None chromosome 4681421 4682149 + probable transcriptional regulator (NCBI) True
PA4186 PA4186 CDS None chromosome 4682242 4683561 + hypothetical protein (NCBI) False
PA4187 PA4187 CDS None chromosome 4683697 4685025 + probable major facilitator superfamily (MFS) transporter (NCBI) False
PA4188 PA4188 CDS None chromosome 4685090 4686001 + hypothetical protein (NCBI) False
PA4189 PA4189 CDS None chromosome 4685994 4687484 + probable aldehyde dehydrogenase (NCBI) False
PA4597 oprJ CDS None chromosome 5149633 5151072 - Multidrug efflux outer membrane protein OprJ precursor (NCBI) False
PA4598 mexD CDS None chromosome 5151078 5154209 - Resistance-Nodulation-Cell Division (RND) multidrug efflux transporter MexD (NCBI) False
PA4599 mexC CDS None chromosome 5154237 5155400 - Resistance-Nodulation-Cell Division (RND) multidrug efflux membrane fusion protein MexC precursor (NCBI) False
PA4600 nfxB CDS None chromosome 5155561 5156124 + transcriptional regulator NfxB (NCBI) True
PA4977 PA4977 CDS None chromosome 5587574 5589253 - probable acetolactate synthase large subunit (NCBI) False
PA4978 PA4978 CDS None chromosome 5589295 5591385 - hypothetical protein (NCBI) False
PA4979 PA4979 CDS None chromosome 5591452 5592612 - probable acyl-CoA dehydrogenase (NCBI) False
PA4980 PA4980 CDS None chromosome 5592633 5593424 - probable enoyl-CoA hydratase/isomerase (NCBI) False
PA5530 PA5530 CDS None chromosome 6223174 6224481 + probable MFS dicarboxylate transporter (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.