Organism : Pseudomonas aeruginosa | Module List:
Module 505 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 505

There are 25 regulatory influences for Module 505

Regulator Table (25)
Regulator Name Type
PA2320 tf
PA1099 tf
PA3583 tf
PA2259 tf
PA2879 tf
PA1138 tf
PA4227 tf
PA1945 tf
PA0416 tf
PA1713 tf
PA0816 tf
PA0512 tf
PA1663 tf
PA5059 tf
PA4296 tf
PA2692 tf
PA4462 tf
PA1283 tf
PA2484 tf
PA3458 tf
PA2050 tf
PA4135 tf
PA2846 tf
PA1912 tf
PA3197 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
3824 3.50e-10 atttttT.tgtttagAAaatAat
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3825 8.70e-09 AcAACaAtAagaaaGaGacGaCc
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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 505 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 0.00e+00 0.00e+00 17/25
Carbohydrate Metabolism kegg subcategory 0.00e+00 0.00e+00 13/25
Glycolysis / Gluconeogenesis kegg pathway 1.70e-05 2.48e-04 3/25
Pentose phosphate pathway kegg pathway 0.00e+00 0.00e+00 7/25
Glyoxylate and dicarboxylate metabolism kegg pathway 0.00e+00 8.00e-06 4/25
Energy Metabolism kegg subcategory 7.95e-03 1.96e-02 3/25
Methane metabolism kegg pathway 1.10e-05 1.67e-04 3/25
Global kegg category 0.00e+00 0.00e+00 16/25
Metabolism kegg subcategory 0.00e+00 0.00e+00 16/25
Metabolic pathways kegg pathway 0.00e+00 0.00e+00 16/25
Biosynthesis of secondary metabolites kegg pathway 4.60e-05 5.25e-04 7/25
Microbial metabolism in diverse environments kegg pathway 0.00e+00 0.00e+00 13/25

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 10/25
Electron transport tigr sub1role 5.50e-05 1.19e-04 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 0.00e+00 0.00e+00 22/25
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 10/25
Carbohydrate transport and metabolism cog subcategory 0.00e+00 0.00e+00 9/25
Amino acid transport and metabolism cog subcategory 1.87e-02 2.99e-02 5/25
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 505

There are 25 genes in Module 505

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0035 trpA CDS None chromosome 37087 37893 - tryptophan synthase alpha chain (NCBI) False
PA0036 trpB CDS None chromosome 37890 39098 - tryptophan synthase subunit beta (NCBI) False
PA2264 PA2264 CDS None chromosome 2493218 2493934 + hypothetical protein (NCBI) False
PA2265 PA2265 CDS None chromosome 2493937 2495712 + gluconate dehydrogenase (NCBI) False
PA2266 PA2266 CDS None chromosome 2495724 2497043 + probable cytochrome c precursor (NCBI) False
PA2320 gntR CDS None chromosome 2558918 2559949 - transcriptional regulator GntR (NCBI) True
PA2321 PA2321 CDS None chromosome 2560144 2560665 + gluconokinase (NCBI) False
PA2322 PA2322 CDS None chromosome 2560762 2562114 + gluconate permease (NCBI) False
PA2323 PA2323 CDS None chromosome 2562447 2564072 + probable glyceraldehyde-3-phosphate dehydrogenase (NCBI) False
PA2481 PA2481 CDS None chromosome 2799910 2800785 - hypothetical protein (NCBI) False
PA2482 PA2482 CDS None chromosome 2800782 2801435 - probable cytochrome c (NCBI) False
PA2483 PA2483 CDS None chromosome 2801550 2802551 - hypothetical protein (NCBI) False
PA3181 PA3181 CDS None chromosome 3570941 3571603 - keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase (NCBI) False
PA3182 pgl CDS None chromosome 3571621 3572337 - 6-phosphogluconolactonase (NCBI) False
PA3183 zwf CDS None chromosome 3572324 3573793 - glucose-6-phosphate 1-dehydrogenase (NCBI) False
PA3192 gltR CDS None chromosome 3583616 3584344 - two-component response regulator GltR (NCBI) False
PA3193 glk CDS None chromosome 3584379 3585374 - glucokinase (NCBI) False
PA3194 edd CDS None chromosome 3585477 3587303 - phosphogluconate dehydratase (NCBI) False
PA3195 gapA CDS None chromosome 3587433 3588437 + glyceraldehyde 3-phosphate dehydrogenase (NCBI) False
PA3581 glpF CDS None chromosome 4012806 4013645 + glycerol uptake facilitator protein (NCBI) False
PA3582 glpK CDS None chromosome 4013685 4015202 + glycerol kinase (NCBI) False
PA3584 glpD CDS None chromosome 4016441 4017979 + glycerol-3-phosphate dehydrogenase (NCBI) False
PA4810 fdnI CDS None chromosome 5396992 5397618 - nitrate-inducible formate dehydrogenase, gamma subunit (NCBI) False
PA4811 fdnH CDS None chromosome 5397690 5398619 - nitrate-inducible formate dehydrogenase, beta subunit (NCBI) False
PA4812 fdnG CDS None chromosome 5398628 5401708 - formate dehydrogenase-O (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 505

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.