Organism : Pseudomonas aeruginosa | Module List:
Module 380 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 380

There are 25 regulatory influences for Module 380

Regulator Table (25)
Regulator Name Type
PA0167 tf
PA1335 tf
PA0125 tf
PA1397 tf
PA4270 tf
PA5253 tf
PA0890 tf
PA3804 tf
PA3002 tf
PA2591 tf
PA4493 tf
PA1859 tf
PA1430 tf
PA0893 tf
PA1300 tf
PA3699 tf
PA1760 tf
PA5403 tf
PA3714 tf
PA0393 tf
PA2577 tf
PA2917 tf
PA1945 tf
PA1980 tf
PA2588 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
3584 1.70e-01 CgcTggaaatcTttgaccgaTccc
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3585 4.00e+03 tTtcggaAatgCgacaggAA
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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 380 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 2.16e-03 8.23e-03 11/29
Nucleotide Metabolism kegg subcategory 1.61e-03 6.87e-03 3/29
Purine metabolism kegg pathway 5.96e-04 3.57e-03 3/29
Amino Acid Metabolism kegg subcategory 2.40e-05 3.20e-04 8/29
Arginine and proline metabolism kegg pathway 0.00e+00 0.00e+00 8/29
Xenobiotics Biodegradation and Metabolism kegg subcategory 1.86e-03 7.49e-03 3/29
Atrazine degradation kegg pathway 0.00e+00 0.00e+00 3/29
Environmental Information Processing kegg category 6.17e-03 1.64e-02 6/29
Membrane Transport kegg subcategory 5.72e-04 3.48e-03 6/29
ABC transporters kegg pathway 5.70e-05 6.27e-04 6/29
Microbial metabolism in diverse environments kegg pathway 1.46e-02 3.04e-02 4/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Central intermediary metabolism tigr mainrole 3.00e-06 8.00e-06 4/29
Nitrogen metabolism tigr sub1role 0.00e+00 0.00e+00 4/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 2.20e-03 4.03e-03 4/29
Amino acid transport and metabolism cog subcategory 1.70e-05 6.10e-05 10/29
General function prediction only cog subcategory 8.22e-03 1.38e-02 7/29
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 380

There are 29 genes in Module 380

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0305 PA0305 CDS None chromosome 344303 346690 - hypothetical protein (NCBI) False
PA0895 aruC CDS None chromosome 977910 979130 + N-succinylglutamate 5-semialdehyde dehydrogenase (NCBI) False
PA0896 aruF CDS None chromosome 979329 980345 + arginine/ornithine succinyltransferase AI subunit (NCBI) False
PA0897 aruG CDS None chromosome 980357 981379 + arginine/ornithine succinyltransferase AII subunit (NCBI) False
PA0898 aruD CDS None chromosome 981422 982888 + succinylglutamate 5-semialdehyde dehydrogenase (NCBI) False
PA0899 aruB CDS None chromosome 982885 984231 + succinylarginine dihydrolase (NCBI) False
PA1005 PA1005 CDS None chromosome 1089010 1090443 - hypothetical protein (NCBI) False
PA1807 PA1807 CDS None chromosome 1962046 1963656 - probable ATP-binding component of ABC transporter (NCBI) False
PA1808 PA1808 CDS None chromosome 1963658 1964677 - probable permease of ABC transporter (NCBI) False
PA1809 PA1809 CDS None chromosome 1964682 1965764 - probable permease of ABC transporter (NCBI) False
PA1810 PA1810 CDS None chromosome 1965771 1967618 - probable binding protein component of ABC transporter (NCBI) False
PA1811 PA1811 CDS None chromosome 1967615 1969444 - probable solute-binding protein (NCBI) False
PA3438 folE1 CDS None chromosome 3845775 3846335 + GTP cyclohydrolase I precursor (NCBI) False
PA3439 folX CDS None chromosome 3846337 3846708 + d-erythro-7,8-dihydroneopterin triphosphate epimerase (NCBI) False
PA3693 PA3693 CDS None chromosome 4135452 4135973 - hypothetical protein (NCBI) False
PA3694 PA3694 CDS None chromosome 4135970 4136293 - hypothetical protein (NCBI) False
PA3695 PA3695 CDS None chromosome 4136290 4137195 - hypothetical protein (NCBI) False
PA3696 PA3696 CDS None chromosome 4137192 4137938 - hypothetical protein (NCBI) False
PA3934 PA3934 CDS None chromosome 4410993 4413029 - hypothetical protein (NCBI) False
PA4375 PA4375 CDS None chromosome 4904647 4907703 + probable RND efflux transporter (NCBI) False
PA4864 ureD CDS None chromosome 5462763 5463605 + urease accessory protein (NCBI) False
PA4865 ureA CDS None chromosome 5463607 5463909 + urease gamma subunit (NCBI) False
PA4866 PA4866 CDS None chromosome 5463918 5464436 + hypothetical protein (NCBI) False
PA4867 ureB CDS None chromosome 5464453 5464758 + urease beta subunit (NCBI) False
PA4868 ureC CDS None chromosome 5464821 5466521 + urease alpha subunit (NCBI) False
PA4891 ureE CDS None chromosome 5487215 5487718 + urease accessory protein UreE (NCBI) False
PA4893 ureG CDS None chromosome 5488397 5489011 + urease accessory protein UreG (NCBI) False
PA4894 PA4894 CDS None chromosome 5489041 5489613 + hypothetical protein (NCBI) False
PA5317 PA5317 CDS None chromosome 5986475 5988055 + probable binding protein component of ABC dipeptide 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.

Comments for Module 380

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.