Organism : Pseudomonas aeruginosa | Module List:
Module 49 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 49

There are 11 regulatory influences for Module 49

Regulator Table (11)
Regulator Name Type
PA1335 tf
PA5166 tf
PA0167 tf
PA4269 tf
PA3002 tf
PA0893 tf
PA4493 tf
PA4109 tf
PA4462 tf
PA0125 tf
PA0159 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
2930 1.50e+03 CgGGGAaAAc
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2931 1.80e+04 AATTGtTTACAT
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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 49 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Cofactors and Vitamins kegg subcategory 1.17e-02 2.57e-02 3/32
Porphyrin and chlorophyll metabolism kegg pathway 1.15e-04 1.07e-03 3/32
Genetic Information Processing kegg category 2.55e-03 9.28e-03 5/32
Replication and Repair kegg subcategory 8.00e-06 1.35e-04 4/32
Homologous recombination kegg pathway 7.00e-06 1.26e-04 3/32
Signal Transduction kegg subcategory 1.02e-02 2.33e-02 3/32
Two-component system kegg pathway 1.02e-02 2.33e-02 3/32

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA metabolism tigr mainrole 0.00e+00 0.00e+00 6/32
DNA replication, recombination, and repair tigr sub1role 0.00e+00 0.00e+00 6/32
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 3.66e-03 5.18e-03 3/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 9.35e-03 1.55e-02 9/32
Replication, recombination and repair cog subcategory 6.00e-06 2.50e-05 6/32
Coenzyme transport and metabolism cog subcategory 3.96e-03 6.99e-03 4/32
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 49

There are 32 genes in Module 49

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0159 PA0159 CDS None chromosome 182768 183706 + probable transcriptional regulator (NCBI) True
PA0927 ldhA CDS None chromosome 1011983 1012972 - D-lactate dehydrogenase (fermentative) (NCBI) False
PA1335 PA1335 CDS None chromosome 1447226 1448503 - probable two-component response regulator (NCBI) True
PA1336 PA1336 CDS None chromosome 1448548 1450449 - probable two-component sensor (NCBI) False
PA1726 bglX CDS None chromosome 1866241 1868535 - periplasmic beta-glucosidase (NCBI) False
PA1811 PA1811 CDS None chromosome 1967615 1969444 - probable solute-binding protein (NCBI) False
PA2529 PA2529 CDS None chromosome 2855548 2856981 + hypothetical protein (NCBI) False
PA2585 uvrC CDS None chromosome 2923961 2925787 - excinuclease ABC subunit C (NCBI) False
PA2683 PA2683 CDS None chromosome 3030436 3031398 - serine/threonine dehydratase (NCBI) False
PA2873 PA2873 CDS None chromosome 3225381 3227387 - hypothetical protein (NCBI) False
PA2908 cbiD CDS None chromosome 3262762 3263862 + cobalt-precorrin-6A synthase (NCBI) False
PA2909 PA2909 CDS None chromosome 3263859 3264587 + precorrin-6x reductase (NCBI) False
PA2948 cobM CDS None chromosome 3307510 3308262 + precorrin-3 methylase (NCBI) False
PA3074 PA3074 CDS None chromosome 3446255 3448015 + hypothetical protein (NCBI) False
PA3076 PA3076 CDS None chromosome 3449697 3450776 + hypothetical protein (NCBI) False
PA3863 PA3863 CDS None chromosome 4323758 4324885 + hypothetical protein (NCBI) False
PA4109 ampR CDS None chromosome 4592990 4593880 - transcriptional regulator AmpR (NCBI) True
PA4283 recD CDS None chromosome 4799299 4801464 - exodeoxyribonuclease V alpha chain (NCBI) False
PA4284 recB CDS None chromosome 4801461 4805198 - exodeoxyribonuclease V beta chain (NCBI) False
PA4285 recC CDS None chromosome 4805195 4808710 - exodeoxyribonuclease V gamma chain (NCBI) False
PA4579 PA4579 CDS None chromosome 5126713 5128569 + hypothetical protein (NCBI) False
PA4669 ipk CDS None chromosome 5237393 5238241 + 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (NCBI) False
PA4688 hitB CDS None chromosome 5258724 5260262 + iron (III)-transport system permease HitB (NCBI) False
PA4794 PA4794 CDS None chromosome 5381145 5381627 + hypothetical protein (NCBI) False
PA4795 PA4795 CDS None chromosome 5381617 5381994 + hypothetical protein (NCBI) False
PA4796 PA4796 CDS None chromosome 5381991 5382458 + hypothetical protein (NCBI) False
PA4807 selB CDS None chromosome 5392523 5394448 - selenocysteine-specific elongation factor (NCBI) False
PA4863 PA4863 CDS None chromosome 5462302 5462754 + hypothetical protein (NCBI) False
PA4964 parC CDS None chromosome 5572222 5574486 - DNA topoisomerase IV subunit A (NCBI) False
PA4966 PA4966 CDS None chromosome 5575015 5576028 - hypothetical protein (NCBI) False
PA5165 PA5165 CDS None chromosome 5813727 5815565 + probable two-component sensor (NCBI) False
PA5280 sss CDS None chromosome 5944327 5945238 + site-specific recombinase Sss (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 49

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.