Organism : Pseudomonas aeruginosa | Module List:
Module 146 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 146

There are 34 regulatory influences for Module 146

Regulator Table (34)
Regulator Name Type
PA2016 tf
PA1949 tf
PA2115 tf
PA4787 tf
PA2010 tf
PA1430 tf
PA4769 tf
PA4070 tf
PA1713 tf
PA2484 tf
PA2020 tf
PA0121 tf
PA4275 tf
PA3565 tf
PA1998 tf
PA2511 tf
PA1099 tf
PA2121 tf
PA1309 tf
PA0893 tf
PA2320 tf
PA0207 tf
PA1633 tf
PA0708 tf
PA0294 tf
PA1760 tf
PA5085 tf
PA1859 tf
PA0512 tf
PA4196 tf
PA3363 tf
PA4132 tf
PA1853 tf
PA1015 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
3122 2.60e+02 TtgTTGAA
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3123 6.90e+03 TGGAAAAACA
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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 146 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 2.50e-05 3.26e-04 11/20
Carbohydrate Metabolism kegg subcategory 7.41e-03 1.85e-02 3/20
Butanoate metabolism kegg pathway 2.50e-05 3.34e-04 3/20
Energy Metabolism kegg subcategory 3.55e-04 2.45e-03 4/20
Lipid Metabolism kegg subcategory 6.35e-04 3.74e-03 3/20
Synthesis and degradation of ketone bodies kegg pathway 0.00e+00 1.00e-06 3/20
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 11/20
Glycine serine and threonine metabolism kegg pathway 0.00e+00 0.00e+00 5/20
Valine leucine and isoleucine degradation kegg pathway 4.60e-05 5.28e-04 3/20
Tyrosine metabolism kegg pathway 1.00e-06 3.20e-05 3/20
Metabolism of Cofactors and Vitamins kegg subcategory 1.82e-04 1.50e-03 4/20
One carbon pool by folate kegg pathway 0.00e+00 1.00e-05 3/20
Xenobiotics Biodegradation and Metabolism kegg subcategory 4.32e-04 2.87e-03 3/20
Global kegg category 2.33e-04 1.78e-03 9/20
Metabolism kegg subcategory 2.33e-04 1.78e-03 9/20
Metabolic pathways kegg pathway 1.01e-04 9.69e-04 9/20
Biosynthesis of secondary metabolites kegg pathway 4.37e-03 1.31e-02 4/20
Microbial metabolism in diverse environments kegg pathway 3.60e-04 2.48e-03 5/20

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 0.00e+00 0.00e+00 7/20
Amino acids and amines tigr sub1role 0.00e+00 0.00e+00 6/20

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.90e-05 8.80e-05 15/20
Amino acid transport and metabolism cog subcategory 2.00e-06 1.00e-05 9/20
Lipid transport and metabolism cog subcategory 8.13e-03 1.37e-02 3/20
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 146

There are 20 genes in Module 146

Gene Member Table (20)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0049 PA0049 CDS None chromosome 63068 64729 - hypothetical protein (NCBI) False
PA0865 hpd CDS None chromosome 945834 946907 + 4-hydroxyphenylpyruvate dioxygenase (NCBI) False
PA1999 PA1999 CDS None chromosome 2185527 2186225 + probable CoA transferase, subunit A (NCBI) False
PA2000 PA2000 CDS None chromosome 2186260 2186916 + probable CoA transferase, subunit B (NCBI) False
PA2001 atoB CDS None chromosome 2187065 2188246 + acetyl-CoA acetyltransferase (NCBI) False
PA2008 fahA CDS None chromosome 2196129 2197427 - fumarylacetoacetase (NCBI) False
PA2009 hmgA CDS None chromosome 2197432 2198730 - homogentisate 1,2-dioxygenase (NCBI) False
PA2109 PA2109 CDS None chromosome 2320586 2321062 - hypothetical protein (NCBI) False
PA2110 PA2110 CDS None chromosome 2321130 2322071 - hypothetical protein (NCBI) False
PA2111 PA2111 CDS None chromosome 2322068 2322781 - hypothetical protein (NCBI) False
PA2112 PA2112 CDS None chromosome 2322778 2323521 - hypothetical protein (NCBI) False
PA2113 PA2113 CDS None chromosome 2323554 2324783 - probable porin (NCBI) False
PA2114 PA2114 CDS None chromosome 2324808 2326079 - probable major facilitator superfamily (MFS) transporter (NCBI) False
PA2116 PA2116 CDS None chromosome 2327394 2328191 + hypothetical protein (NCBI) False
PA2442 gcvT2 CDS None chromosome 2739762 2740883 - glycine cleavage system protein T2 (NCBI) False
PA2443 sdaA CDS None chromosome 2740977 2742353 - L-serine dehydratase (NCBI) False
PA2444 glyA2 CDS None chromosome 2742401 2743657 - serine hydroxymethyltransferase (NCBI) False
PA2445 gcvP2 CDS None chromosome 2743800 2746679 - glycine cleavage system protein P2 (NCBI) False
PA2446 gcvH2 CDS None chromosome 2746690 2747073 - glycine cleavage system protein H2 (NCBI) False
PA5415 glyA1 CDS None chromosome 6094024 6095277 + serine hydroxymethyltransferase (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 146

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.