Organism : Pseudomonas aeruginosa | Module List:
Module 175 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 175

There are 15 regulatory influences for Module 175

Regulator Table (15)
Regulator Name Type
PA3830 tf
PA1261 tf
PA1128 tf
PA4174 tf
PA5032 tf
PA0217 tf
PA0448 tf
PA4169 tf
PA3757 tf
PA2050 tf
PA2917 tf
PA3249 tf
PA3711 tf
PA0564 tf
PA1526 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
3178 3.80e+02 AtcGgGaaAA
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3179 6.00e+04 AAGTGTCATT
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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 175 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 2.99e-02 3.34e-02 3/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 3.16e-02 4.87e-02 4/31
Carbohydrate transport and metabolism cog subcategory 2.49e-02 3.90e-02 3/31
Nucleotide transport and metabolism cog subcategory 3.15e-03 5.65e-03 3/31
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 175

There are 31 genes in Module 175

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0142 PA0142 CDS None chromosome 161906 163255 + hydroxydechloroatrazine ethylaminohydrolase (NCBI) False
PA0223 PA0223 CDS None chromosome 252913 253794 - probable dihydrodipicolinate synthetase (NCBI) False
PA0448 PA0448 CDS None chromosome 504121 505029 + probable transcriptional regulator (NCBI) True
PA0550 PA0550 CDS None chromosome 609202 609999 - hypothetical protein (NCBI) False
PA0600 PA0600 CDS None chromosome 660315 662708 + probable two-component sensor (NCBI) False
PA1113 PA1113 CDS None chromosome 1205771 1207537 + probable ATP-binding/permease fusion ABC transporter (NCBI) False
PA1128 PA1128 CDS None chromosome 1220745 1221656 + probable transcriptional regulator (NCBI) True
PA1158 PA1158 CDS None chromosome 1256094 1257452 + probable two-component sensor (NCBI) False
PA1334 PA1334 CDS None chromosome 1445806 1446918 - probable oxidoreductase (NCBI) False
PA1406 PA1406 CDS None chromosome 1528803 1529561 - hypothetical protein (NCBI) False
PA1646 PA1646 CDS None chromosome 1791080 1793038 + probable chemotaxis transducer (NCBI) False
PA1820 nhaB CDS None chromosome 1978439 1979941 - sodium/proton antiporter NhaB (NCBI) False
PA1825 PA1825 CDS None chromosome 1984389 1985033 + hypothetical protein (NCBI) False
PA1906 PA1906 CDS None chromosome 2077047 2077583 - hypothetical protein (NCBI) False
PA2521 czcB CDS None chromosome 2840512 2841966 - Resistance-Nodulation-Cell Division (RND) divalent metal cation efflux membrane fusion protein CzcB precursor (NCBI) False
PA2688 pfeA CDS None chromosome 3040242 3042482 + Ferric enterobactin receptor, outer membrane protein PfeA precursor (NCBI) False
PA2917 PA2917 CDS None chromosome 3272457 3273293 - probable transcriptional regulator (NCBI) True
PA3206 PA3206 CDS None chromosome 3595942 3597279 + probable two-component sensor (NCBI) False
PA3464 PA3464 CDS None chromosome 3874654 3875979 - hypothetical protein (NCBI) False
PA3605 PA3605 CDS None chromosome 4039174 4040100 + hypothetical protein (NCBI) False
PA3733 PA3733 CDS None chromosome 4183710 4184939 + hypothetical protein (NCBI) False
PA3749 PA3749 CDS None chromosome 4201252 4202565 + probable major facilitator superfamily (MFS) transporter (NCBI) False
PA3783 PA3783 CDS None chromosome 4242416 4243045 + hypothetical protein (NCBI) False
PA3830 PA3830 CDS None chromosome 4287794 4288606 - probable transcriptional regulator (NCBI) True
PA3927 PA3927 CDS None chromosome 4402638 4403426 + probable transcriptional regulator (NCBI) True
PA3960 PA3960 CDS None chromosome 4439377 4439784 + hypothetical protein (NCBI) False
PA4082 cupB5 CDS None chromosome 4561540 4564596 - adhesive protein CupB5 (NCBI) False
PA4146 PA4146 CDS None chromosome 4638887 4639291 + hypothetical protein (NCBI) False
PA4167 PA4167 CDS None chromosome 4662693 4663511 - probable oxidoreductase (NCBI) False
PA4804 PA4804 CDS None chromosome 5388702 5390099 - probable amino acid permease (NCBI) False
PA5292 pchP CDS None chromosome 5957208 5958257 - phosphorylcholine phosphatase (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 175

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.