Organism : Pseudomonas aeruginosa | Module List:
Module 491 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 491

There are 24 regulatory influences for Module 491

Regulator Table (24)
Regulator Name Type
PA5380 tf
PA4436 tf
PA0797 tf
PA1760 tf
PA4853 tf
PA1978 tf
PA4769 tf
PA0149 tf
PA2376 tf
PA3895 tf
PA1949 tf
PA5189 tf
PA4196 tf
PA0533 tf
PA2056 tf
PA1159 tf
PA1853 tf
PA2551 tf
PA1759 tf
PA2020 tf
PA2121 tf
PA2917 tf
PA4354 tf
PA5428 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
3796 2.30e-09 acaacAA.aAcAA.aagag
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3797 2.00e+02 attccCtt.caaaaaGaaAAcat
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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 491 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Environmental Information Processing kegg category 0.00e+00 1.20e-05 11/28
Membrane Transport kegg subcategory 7.00e-06 1.24e-04 8/28
ABC transporters kegg pathway 0.00e+00 9.00e-06 8/28
Signal Transduction kegg subcategory 6.34e-03 1.67e-02 3/28
Two-component system kegg pathway 6.34e-03 1.67e-02 3/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 6.80e-05 1.46e-04 6/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.37e-02 3.73e-02 14/28
Carbohydrate transport and metabolism cog subcategory 1.76e-02 2.82e-02 3/28
Amino acid transport and metabolism cog subcategory 7.70e-05 1.98e-04 9/28
Inorganic ion transport and metabolism cog subcategory 1.68e-02 2.70e-02 4/28
ABC-type dipeptide transport system, periplasmic component cog 0.00e+00 0.00e+00 4/28
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 491

There are 28 genes in Module 491

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0887 acsA CDS None chromosome 969670 971625 + acetyl-coenzyme A synthetase (NCBI) False
PA1818 PA1818 CDS None chromosome 1974821 1977076 + probable Orn/Arg/Lys decarboxylase (NCBI) False
PA1991 PA1991 CDS None chromosome 2176974 2178137 + probable iron-containing alcohol dehydrogenase (NCBI) False
PA1992 PA1992 CDS None chromosome 2178121 2179815 + probable two-component sensor (NCBI) False
PA2862 lipA CDS None chromosome 3214282 3215217 + lactonizing lipase precursor (NCBI) False
PA3038 PA3038 CDS None chromosome 3400684 3401949 + probable porin (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
PA3234 actP CDS None chromosome 3621505 3623160 - acetate permease (NCBI) False
PA3235 PA3235 CDS None chromosome 3623157 3623468 - hypothetical protein (NCBI) False
PA4496 PA4496 CDS None chromosome 5031488 5033101 + probable binding protein component of ABC transporter (NCBI) False
PA4497 PA4497 CDS None chromosome 5033194 5034792 + probable binding protein component of ABC transporter (NCBI) False
PA4500 PA4500 CDS None chromosome 5037074 5038675 + probable binding protein component of ABC transporter (NCBI) False
PA4501 PA4501 CDS None chromosome 5038901 5040355 + probable porin (NCBI) False
PA4502 PA4502 CDS None chromosome 5040405 5042000 + probable binding protein component of ABC transporter (NCBI) False
PA4503 PA4503 CDS None chromosome 5042068 5043078 + probable permease of ABC transporter (NCBI) False
PA4504 PA4504 CDS None chromosome 5043090 5044001 + probable permease of ABC transporter (NCBI) False
PA4505 PA4505 CDS None chromosome 5044054 5045028 + probable ATP-binding component of ABC transporter (NCBI) False
PA4506 PA4506 CDS None chromosome 5045028 5045999 + probable ATP-binding component of ABC dipeptide transporter (NCBI) False
PA5167 PA5167 CDS None chromosome 5817191 5818186 + probable c4-dicarboxylate-binding protein (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
PA5380 PA5380 CDS None chromosome 6058673 6059776 + probable transcriptional regulator (NCBI) True
PA5542 PA5542 CDS None chromosome 6234500 6235744 - hypothetical protein (NCBI) False
PA5543 PA5543 CDS None chromosome 6235831 6236229 - hypothetical protein (NCBI) False
PA5545 PA5545 CDS None chromosome 6238325 6239284 - 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 491

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.