Organism : Pseudomonas aeruginosa | Module List:
Module 9 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 9

There are 13 regulatory influences for Module 9

Regulator Table (13)
Regulator Name Type
PA4462 tf
PA4784 tf
PA1607 tf
PA1653 tf
PA2028 tf
PA3699 tf
PA1015 tf
PA2054 tf
PA0906 tf
PA2577 tf
PA2713 tf
PA3689 tf
PA1859 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
2854 4.00e+04 AaacctactTTTaTGCGtt
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2855 8.70e+01 A..cTttgctttgtA.GgaAtatt
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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 9 is enriched for following functions.

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 9

There are 34 genes in Module 9

Gene Member Table (34)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0195 pntA CDS None chromosome 224101 225219 + putative NAD(P) transhydrogenase subunit alpha 1 (NCBI) False
PA0196 pntB CDS None chromosome 225603 227039 + pyridine nucleotide transhydrogenase, beta subunit (NCBI) False
PA0257 PA0257 CDS None chromosome 288384 289175 - hypothetical protein (NCBI) False
PA0258 PA0258 CDS None chromosome 289205 289390 - hypothetical protein (NCBI) False
PA0320 PA0320 CDS None chromosome 359982 360332 + hypothetical protein (NCBI) False
PA0422 PA0422 CDS None chromosome 470081 470650 + hypothetical protein (NCBI) False
PA0423 PA0423 CDS None chromosome 470662 471237 + hypothetical protein (NCBI) False
PA0542 PA0542 CDS None chromosome 599757 600176 - hypothetical protein (NCBI) False
PA0599 PA0599 CDS None chromosome 659102 660163 - hypothetical protein (NCBI) False
PA1182 PA1182 CDS None chromosome 1283176 1284177 - probable transcriptional regulator (NCBI) True
PA1263 PA1263 CDS None chromosome 1371738 1372682 + hypothetical protein (NCBI) False
PA1859 PA1859 CDS None chromosome 2018803 2019690 - probable transcriptional regulator (NCBI) True
PA1863 modA CDS None chromosome 2022411 2023166 - molybdate-binding periplasmic protein precursor ModA (NCBI) False
PA1898 qscR CDS None chromosome 2069490 2070203 + quorum-sensing control repressor (NCBI) True
PA1934 PA1934 CDS None chromosome 2115885 2116265 + hypothetical protein (NCBI) False
PA1942 PA1942 CDS None chromosome 2126104 2126334 - hypothetical protein (NCBI) False
PA2128 cupA1 CDS None chromosome 2342493 2343044 + fimbrial subunit CupA1 (NCBI) False
PA2541 PA2541 CDS None chromosome 2869392 2870027 - probable CDP-alcohol phosphatidyltransferase (NCBI) False
PA2813 PA2813 CDS None chromosome 3166547 3167167 - probable glutathione S-transferase (NCBI) False
PA2943 PA2943 CDS None chromosome 3299492 3300586 + phospho-2-dehydro-3-deoxyheptonate aldolase (NCBI) False
PA3030 mobA CDS None chromosome 3394088 3394684 + molybdopterin-guanine dinucleotide biosynthesis protein A (NCBI) False
PA3055 PA3055 CDS None chromosome 3420309 3420785 - hypothetical protein (NCBI) False
PA3469 PA3469 CDS None chromosome 3882441 3882983 + hypothetical protein (NCBI) False
PA3470 PA3470 CDS None chromosome 3882980 3883438 + hypothetical protein (NCBI) False
PA3575 PA3575 CDS None chromosome 4007507 4008037 + hypothetical protein (NCBI) False
PA3779 PA3779 CDS None chromosome 4237693 4238733 + hypothetical protein (NCBI) False
PA4114 PA4114 CDS None chromosome 4601574 4602083 - spermidine acetyltransferase (NCBI) False
PA4139 PA4139 CDS None chromosome 4629944 4630243 + hypothetical protein (NCBI) False
PA4625 PA4625 CDS None chromosome 5186411 5192875 - hypothetical protein (NCBI) False
PA4784 PA4784 CDS None chromosome 5371800 5372267 + probable transcriptional regulator (NCBI) True
PA5122 PA5122 CDS None chromosome 5770937 5771458 + hypothetical protein (NCBI) False
PA5233 PA5233 CDS None chromosome 5891109 5891528 - flagellar protein (NCBI) False
PA5428 PA5428 CDS None chromosome 6108176 6109084 - probable transcriptional regulator (NCBI) True
PA5533 PA5533 CDS None chromosome 6227082 6227450 + 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 9

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.