Organism : Pseudomonas aeruginosa | Module List:
Module 381 Profile

GeneModule member RegulatorRegulator MotifMotif
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 381

There are 13 regulatory influences for Module 381

Regulator Table (13)
Regulator Name Type
PA5253 tf
PA3622 tf
PA4269 tf
PA0125 tf
PA4462 tf
PA2047 tf
PA3458 tf
PA4493 tf
PA0393 tf
PA2737 tf
PA5437 tf
PA3879 tf
PA0236 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
3586 1.60e+03 GaAGA.Aa
Loader icon
3587 6.60e+03 TTGaTTaaTGcCTGaTTATT
Loader icon
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 381 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 7.00e-06 1.15e-04 12/21
Carbohydrate Metabolism kegg subcategory 0.00e+00 0.00e+00 10/21
Glycolysis / Gluconeogenesis kegg pathway 8.00e-06 1.36e-04 3/21
Glyoxylate and dicarboxylate metabolism kegg pathway 7.00e-06 1.11e-04 3/21
Energy Metabolism kegg subcategory 3.90e-05 4.64e-04 5/21
Methane metabolism kegg pathway 0.00e+00 0.00e+00 5/21
Amino Acid Metabolism kegg subcategory 6.01e-03 1.60e-02 4/21
Valine leucine and isoleucine biosynthesis kegg pathway 3.00e-06 5.00e-05 3/21
Global kegg category 1.00e-06 2.40e-05 12/21
Metabolism kegg subcategory 1.00e-06 2.40e-05 12/21
Metabolic pathways kegg pathway 3.00e-06 6.10e-05 11/21
Biosynthesis of secondary metabolites kegg pathway 1.00e-05 1.66e-04 7/21
Microbial metabolism in diverse environments kegg pathway 5.00e-06 8.70e-05 7/21

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 5.00e-05 1.09e-04 5/21
Electron transport tigr sub1role 2.70e-05 6.20e-05 3/21
Amino acid biosynthesis tigr mainrole 1.72e-04 3.35e-04 3/21
Pyruvate family tigr sub1role 0.00e+00 0.00e+00 3/21

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.31e-02 3.63e-02 11/21
Energy production and conversion cog subcategory 5.11e-03 8.86e-03 4/21
Carbohydrate transport and metabolism cog subcategory 6.27e-03 1.07e-02 3/21
Amino acid transport and metabolism cog subcategory 3.22e-02 4.95e-02 4/21
General function prediction only cog subcategory 1.79e-02 2.87e-02 5/21
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 381

There are 21 genes in Module 381

Gene Member Table (21)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0660 PA0660 CDS None chromosome 713279 714247 - hypothetical protein (NCBI) False
PA0830 PA0830 CDS None chromosome 904768 905601 - hypothetical protein (NCBI) False
PA2290 gcd CDS None chromosome 2518693 2521104 - glucose dehydrogenase (NCBI) False
PA2318 PA2318 CDS None chromosome 2556293 2556658 + hypothetical protein (NCBI) False
PA3120 leuD CDS None chromosome 3502642 3503280 - isopropylmalate isomerase small subunit (NCBI) False
PA3121 leuC CDS None chromosome 3503292 3504716 - isopropylmalate isomerase large subunit (NCBI) False
PA3529 PA3529 CDS None chromosome 3948991 3949593 - probable peroxidase (NCBI) False
PA3628 PA3628 CDS None chromosome 4062970 4063821 - probable esterase (NCBI) False
PA3629 adhC CDS None chromosome 4063875 4064987 - alcohol dehydrogenase class III (NCBI) False
PA3792 leuA CDS None chromosome 4250942 4252606 + 2-isopropylmalate synthase (RefSeq) False
PA3882 PA3882 CDS None chromosome 4348666 4349415 + hypothetical protein (NCBI) False
PA3919 PA3919 CDS None chromosome 4387336 4388727 - hypothetical protein (NCBI) False
PA4329 pykA CDS None chromosome 4856960 4858411 + pyruvate kinase (NCBI) False
PA4336 PA4336 CDS None chromosome 4864994 4865578 - hypothetical protein (NCBI) False
PA4732 pgi CDS None chromosome 5313676 5315340 + glucose-6-phosphate isomerase (NCBI) False
PA4808 selA CDS None chromosome 5394445 5395851 - selenocysteine synthase (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
PA4936 PA4936 CDS None chromosome 5537953 5538699 - probable rRNA methylase (NCBI) False
PA4937 rnr CDS None chromosome 5538696 5541410 - exoribonuclease RNase R (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.

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.