Organism : Pseudomonas aeruginosa | Module List:
Module 253 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 253

There are 15 regulatory influences for Module 253

Regulator Table (15)
Regulator Name Type
PA3804 tf
PA5562 tf
PA0116 tf
PA3094 tf
PA5342 tf
PA4906 tf
PA0873 tf
PA0393 tf
PA0191 tf
PA3477 tf
PA2423 tf
PA1050 tf
PA3126 tf
PA4547 tf
PA0893 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
3334 3.70e-02 GgTAtaaTgcggcGc..ttcc
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3335 1.10e+01 aGccTT..CcCCg.CC.gCCGc
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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 253 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Unknown function tigr mainrole 1.95e-03 2.98e-03 3/35
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 5.09e-03 6.90e-03 3/35

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 2.50e-02 3.92e-02 6/35
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 253

There are 35 genes in Module 253

Gene Member Table (35)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0116 PA0116 CDS None chromosome 136518 136991 + hypothetical protein (NCBI) True
PA0501 bioF CDS None chromosome 560808 562013 + 8-amino-7-oxononanoate synthase (NCBI) False
PA0502 PA0502 CDS None chromosome 562006 562728 + probable biotin biosynthesis protein bioH (NCBI) False
PA0504 bioD CDS None chromosome 563549 564235 + dithiobiotin synthetase (NCBI) False
PA0556 PA0556 CDS None chromosome 614468 614950 + hypothetical protein (NCBI) False
PA0658 PA0658 CDS None chromosome 711220 712020 - probable short-chain dehydrogenase (NCBI) False
PA0935 PA0935 CDS None chromosome 1025401 1026231 + hypothetical protein (NCBI) False
PA0951 PA0951 CDS None chromosome 1037650 1038885 + probable ribonuclease (NCBI) False
PA1050 PA1050 CDS None chromosome 1137043 1138155 + hypothetical protein (NCBI) True
PA1679 PA1679 CDS None chromosome 1828931 1829710 - hypothetical protein (NCBI) False
PA1682 PA1682 CDS None chromosome 1832014 1833165 + probable MFS metabolite transporter (NCBI) False
PA1685 masA CDS None chromosome 1834393 1835142 + enolase-phosphatase E-1 (NCBI) False
PA1973 pqqF CDS None chromosome 2155374 2157701 + pyrroloquinoline quinone biosynthesis protein F (NCBI) False
PA3071 PA3071 CDS None chromosome 3443814 3444752 + hypothetical protein (NCBI) False
PA3075 PA3075 CDS None chromosome 3448012 3449643 + hypothetical protein (NCBI) False
PA3087 PA3087 CDS None chromosome 3465093 3466073 - hypothetical protein (NCBI) False
PA3241 PA3241 CDS None chromosome 3628430 3629599 - hypothetical protein (NCBI) False
PA3683 PA3683 CDS None chromosome 4124858 4125724 - hypothetical protein (NCBI) False
PA3750 PA3750 CDS None chromosome 4202573 4203322 - hypothetical protein (NCBI) False
PA3853 PA3853 CDS None chromosome 4313763 4314452 - probable transferase (NCBI) False
PA3963 PA3963 CDS None chromosome 4442958 4443854 + probable transporter (NCBI) False
PA4347 PA4347 CDS None chromosome 4875638 4876792 - hypothetical protein (NCBI) False
PA4398 PA4398 CDS None chromosome 4927998 4930094 + probable two-component sensor (NCBI) False
PA4906 PA4906 CDS None chromosome 5505071 5505784 - probable transcriptional regulator (NCBI) True
PA4992 PA4992 CDS None chromosome 5607668 5608480 + hypothetical protein (NCBI) False
PA5022 PA5022 CDS None chromosome 5649522 5652878 + hypothetical protein (NCBI) False
PA5179 PA5179 CDS None chromosome 5830924 5831805 + probable transcriptional regulator (NCBI) True
PA5198 PA5198 CDS None chromosome 5850239 5851162 + LD-carboxypeptidase (NCBI) False
PA5199 envZ CDS None chromosome 5851239 5852558 - two-component sensor EnvZ (NCBI) False
PA5200 ompR CDS None chromosome 5852653 5853396 - two-component response regulator OmpR (NCBI) False
PA5202 PA5202 CDS None chromosome 5855936 5856325 + hypothetical protein (NCBI) False
PA5281 PA5281 CDS None chromosome 5945235 5945933 + probable hydrolase (NCBI) False
PA5318 PA5318 CDS None chromosome 5988081 5988629 + hypothetical protein (NCBI) False
PA5342 PA5342 CDS None chromosome 6010258 6011058 - probable transcriptional regulator (NCBI) True
PA5343 PA5343 CDS None chromosome 6011058 6011909 - 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 253

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.