Organism : Pseudomonas aeruginosa | Module List:
Module 406 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 406

There are 38 regulatory influences for Module 406

Regulator Table (38)
Regulator Name Type
PA3932 tf
PA2359 tf
PA2312 tf
PA2423 tf
PA1599 tf
PA1630 tf
PA0191 tf
PA1504 tf
PA0133 tf
PA4703 tf
PA1998 tf
PA4436 tf
PA5506 tf
PA2258 tf
PA5374 tf
PA3845 tf
PA0243 tf
PA4185 tf
PA5525 tf
PA2259 tf
PA3995 tf
PA4508 tf
PA5032 tf
PA0764 tf
PA2846 tf
PA1859 tf
PA4530 tf
PA2489 tf
PA2334 tf
PA2100 tf
PA2588 tf
PA0876 tf
PA2123 tf
PA3583 tf
PA4831 tf
PA1138 tf
PA0167 tf
PA0472 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
3636 3.50e-33 TtaAaAaAtaat.AAttaatAttT
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3637 2.80e-08 ttaTaTTctTT
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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 406 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Energy Metabolism kegg subcategory 1.06e-03 5.19e-03 4/25
Sulfur metabolism kegg pathway 0.00e+00 0.00e+00 4/25
Metabolism of Other Amino Acids kegg subcategory 1.09e-03 5.27e-03 3/25
Environmental Information Processing kegg category 1.14e-02 2.52e-02 5/25
Membrane Transport kegg subcategory 1.47e-03 6.41e-03 5/25
ABC transporters kegg pathway 2.03e-04 1.62e-03 5/25
Microbial metabolism in diverse environments kegg pathway 7.74e-03 1.92e-02 4/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Central intermediary metabolism tigr mainrole 4.20e-05 9.40e-05 3/25
Sulfur metabolism tigr sub1role 0.00e+00 0.00e+00 3/25
Transport and binding proteins tigr mainrole 3.10e-05 7.10e-05 6/25
Anions tigr sub1role 0.00e+00 0.00e+00 4/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 6.23e-03 1.06e-02 14/25
Amino acid transport and metabolism cog subcategory 4.61e-03 8.06e-03 6/25
Inorganic ion transport and metabolism cog subcategory 3.60e-05 1.06e-04 7/25
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 406

There are 25 genes in Module 406

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0191 PA0191 CDS None chromosome 217905 218822 - probable transcriptional regulator (NCBI) True
PA0201 PA0201 CDS None chromosome 229954 230535 + hypothetical protein (NCBI) False
PA0280 cysA CDS None chromosome 313938 314927 - sulfate transport protein CysA (NCBI) False
PA0281 cysW CDS None chromosome 314931 315800 - sulfate transport protein CysW (NCBI) False
PA0282 cysT CDS None chromosome 315811 316629 - sulfate transport protein CysT (NCBI) False
PA0283 sbp CDS None chromosome 316791 317789 - sulfate-binding protein precursor (NCBI) False
PA0284 PA0284 CDS None chromosome 317966 318148 - hypothetical protein (NCBI) False
PA1756 cysH CDS None chromosome 1895692 1896495 - phosphoadenosine phosphosulfate reductase (NCBI) False
PA1837 PA1837 CDS None chromosome 1994667 1995164 - hypothetical protein (NCBI) False
PA1838 cysI CDS None chromosome 1995148 1996806 - sulfite reductase (NCBI) False
PA2062 PA2062 CDS None chromosome 2259478 2260659 + probable pyridoxal-phosphate dependent enzyme (NCBI) False
PA2083 PA2083 CDS None chromosome 2291791 2293065 + probable ring-hydroxylating dioxygenase subunit (NCBI) False
PA2202 PA2202 CDS None chromosome 2421343 2422020 - probable amino acid permease (NCBI) False
PA2203 PA2203 CDS None chromosome 2422022 2422738 - probable amino acid permease (NCBI) False
PA2204 PA2204 CDS None chromosome 2422819 2423625 - probable binding protein component of ABC transporter (NCBI) False
PA2310 PA2310 CDS None chromosome 2548571 2549458 - hypothetical protein (NCBI) False
PA2311 PA2311 CDS None chromosome 2549748 2549906 + hypothetical protein (NCBI) False
PA2359 PA2359 CDS None chromosome 2605937 2607022 - probable transcriptional regulator (NCBI) True
PA3446 PA3446 CDS None chromosome 3851920 3852513 - hypothetical protein (NCBI) False
PA3450 PA3450 CDS None chromosome 3855493 3856131 - probable antioxidant protein (NCBI) False
PA3931 PA3931 CDS None chromosome 4406806 4407585 + hypothetical protein (NCBI) False
PA3932 PA3932 CDS None chromosome 4407760 4408734 + probable transcriptional regulator (NCBI) True
PA4442 cysN CDS None chromosome 4974694 4976595 - binfunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein (NCBI) False
PA4443 cysD CDS None chromosome 4976607 4977524 - sulfate adenylyltransferase subunit 2 (NCBI) False
PA5024 PA5024 CDS None chromosome 5654811 5655527 + 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 406

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.