Organism : Pseudomonas aeruginosa | Module List:
Module 470 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 470

There are 19 regulatory influences for Module 470

Regulator Table (19)
Regulator Name Type
PA5380 tf
PA1978 tf
PA0436 tf
PA5389 tf
PA4914 tf
PA3225 tf
PA4769 tf
PA0816 tf
PA1309 tf
PA3420 tf
PA2320 tf
PA0393 tf
PA1653 tf
PA0707 tf
PA3815 tf
PA3921 tf
PA3249 tf
PA2704 tf
PA2692 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
3756 2.70e+01 aCccAcAAcaACAAagagGA
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3757 7.30e+03 CcgTttCAG
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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 470 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 4.63e-03 1.36e-02 5/28
Glycine serine and threonine metabolism kegg pathway 0.00e+00 3.00e-06 5/28
Environmental Information Processing kegg category 1.07e-03 5.21e-03 7/28
Membrane Transport kegg subcategory 2.75e-03 9.67e-03 5/28
ABC transporters kegg pathway 3.95e-04 2.66e-03 5/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 2.82e-04 5.20e-04 5/28
Amino acids and amines tigr sub1role 2.00e-06 6.00e-06 4/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 9.00e-06 3.70e-05 20/28
Energy production and conversion cog subcategory 3.84e-03 6.79e-03 5/28
Amino acid transport and metabolism cog subcategory 2.00e-06 7.00e-06 11/28
General function prediction only cog subcategory 2.27e-02 3.57e-02 6/28
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 470

There are 28 genes in Module 470

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA1978 PA1978 CDS None chromosome 2163883 2164548 - probable transcriptional regulator (NCBI) True
PA2762 PA2762 CDS None chromosome 3121921 3122265 - hypothetical protein (NCBI) False
PA3079 PA3079 CDS None chromosome 3452872 3455253 - hypothetical protein (NCBI) False
PA3080 PA3080 CDS None chromosome 3455266 3456363 - hypothetical protein (NCBI) False
PA3232 PA3232 CDS None chromosome 3618993 3619619 - DNA polymerase III subunit epsilon (NCBI) False
PA3233 PA3233 CDS None chromosome 3619616 3621415 - hypothetical protein (NCBI) False
PA3236 PA3236 CDS None chromosome 3623686 3624543 - probable glycine betaine-binding protein precursor (NCBI) False
PA4909 PA4909 CDS None chromosome 5507969 5508685 - probable ATP-binding component of ABC transporter (NCBI) False
PA4910 PA4910 CDS None chromosome 5508682 5509554 - probable ATP-binding component of ABC transporter (NCBI) False
PA4911 PA4911 CDS None chromosome 5509551 5510828 - probable permease of ABC branched-chain amino acid transporter (NCBI) False
PA4912 PA4912 CDS None chromosome 5510839 5511753 - probable permease of ABC branched chain amino acid transporter (NCBI) False
PA5168 PA5168 CDS None chromosome 5818202 5818834 + probable dicarboxylate transporter (NCBI) False
PA5169 PA5169 CDS None chromosome 5818831 5820114 + probable C4-dicarboxylate transporter (NCBI) False
PA5379 sdaB CDS None chromosome 6056877 6058253 + L-serine dehydratase (NCBI) False
PA5396 PA5396 CDS None chromosome 6074230 6075207 + hypothetical protein (NCBI) False
PA5397 PA5397 CDS None chromosome 6075334 6075864 + hypothetical protein (NCBI) False
PA5398 PA5398 CDS None chromosome 6075880 6077940 + probable FMN oxidoreductase (NCBI) False
PA5399 PA5399 CDS None chromosome 6078044 6080005 + probable ferredoxin (NCBI) False
PA5400 PA5400 CDS None chromosome 6080370 6081356 + probable electron transfer flavoprotein alpha subunit (NCBI) False
PA5401 PA5401 CDS None chromosome 6081392 6082165 + hypothetical protein (NCBI) False
PA5410 PA5410 CDS None chromosome 6085385 6086674 - probable ring hydroxylating dioxygenase, alpha-subunit (NCBI) False
PA5411 PA5411 CDS None chromosome 6087099 6088199 + probable ferredoxin (NCBI) False
PA5416 soxB CDS None chromosome 6095363 6096613 + sarcosine oxidase beta subunit (NCBI) False
PA5417 soxD CDS None chromosome 6096707 6097027 + sarcosine oxidase delta subunit (NCBI) False
PA5418 soxA CDS None chromosome 6097024 6100041 + sarcosine oxidase alpha subunit (NCBI) False
PA5419 soxG CDS None chromosome 6100135 6100770 + sarcosine oxidase gamma subunit (NCBI) False
PA5420 purU2 CDS None chromosome 6100820 6101677 + formyltetrahydrofolate deformylase (NCBI) False
PA5421 fdhA CDS None chromosome 6101884 6103083 + glutathione-independent formaldehyde dehydrogenase (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 470

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.