Organism : Pseudomonas aeruginosa | Module List:
Module 384 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 384

There are 18 regulatory influences for Module 384

Regulator Table (18)
Regulator Name Type
PA1490 tf
PA3604 tf
PA0961 tf
PA0890 tf
PA0487 tf
PA3948 tf
PA1099 tf
PA4906 tf
PA0167 tf
PA1859 tf
PA4196 tf
PA1290 tf
PA4021 tf
PA0780 tf
PA3899 tf
PA3594 tf
PA3215 tf
PA4462 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
3592 7.90e-01 ATCGaTGaAcGaAaaccgGGaatT
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3593 6.90e+02 CCACttCGCCGacGcaAcccC
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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 384 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Other Amino Acids kegg subcategory 2.19e-03 8.35e-03 3/30
Metabolism of Cofactors and Vitamins kegg subcategory 9.32e-03 2.19e-02 3/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA metabolism tigr mainrole 4.97e-04 8.72e-04 3/30
DNA replication, recombination, and repair tigr sub1role 3.74e-04 6.75e-04 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Coenzyme transport and metabolism cog subcategory 1.73e-02 2.77e-02 3/30
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 384

There are 30 genes in Module 384

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
PA0006 PA0006 CDS None chromosome 7803 8339 - hypothetical protein (NCBI) False
PA0022 PA0022 CDS None chromosome 24001 24558 + hypothetical protein (NCBI) False
PA0706 cat CDS None chromosome 779463 780101 - chloramphenicol acetyltransferase (NCBI) False
PA0735 PA0735 CDS None chromosome 802260 803075 - hypothetical protein (NCBI) False
PA0750 ung CDS None chromosome 818003 818698 + uracil-DNA glycosylase (NCBI) False
PA0827 PA0827 CDS None chromosome 901934 902812 - hypothetical protein (NCBI) False
PA0902 PA0902 CDS None chromosome 985692 986696 + hypothetical protein (NCBI) False
PA0919 PA0919 CDS None chromosome 1002681 1003964 - hypothetical protein (NCBI) False
PA0920 PA0920 CDS None chromosome 1003966 1006611 - hypothetical protein (NCBI) False
PA0921 PA0921 CDS None chromosome 1006860 1007219 + hypothetical protein (NCBI) False
PA1031 PA1031 CDS None chromosome 1118158 1119519 + hypothetical protein (NCBI) False
PA1042 PA1042 CDS None chromosome 1127717 1128016 + hypothetical protein (NCBI) False
PA1043 PA1043 CDS None chromosome 1128009 1128818 + hypothetical protein (NCBI) False
PA1490 PA1490 CDS None chromosome 1617489 1618265 - probable transcriptional regulator (NCBI) True
PA1640 PA1640 CDS None chromosome 1785736 1786773 - hypothetical protein (NCBI) False
PA1685 masA CDS None chromosome 1834393 1835142 + enolase-phosphatase E-1 (NCBI) False
PA1748 PA1748 CDS None chromosome 1889323 1890012 - enoyl-CoA hydratase (NCBI) False
PA1798 PA1798 CDS None chromosome 1950439 1951725 - probable two-component sensor (NCBI) False
PA1799 PA1799 CDS None chromosome 1951726 1952433 - probable two-component response regulator (NCBI) False
PA1840 PA1840 CDS None chromosome 1998587 1998949 + hypothetical protein (NCBI) False
PA2545 xthA CDS None chromosome 2876555 2877367 + exodeoxyribonuclease III (NCBI) False
PA2947 PA2947 CDS None chromosome 3307085 3307513 + hypothetical protein (NCBI) False
PA3338 PA3338 CDS None chromosome 3747166 3747456 - hypothetical protein (NCBI) False
PA3992 PA3992 CDS None chromosome 4472131 4473477 + hypothetical protein (NCBI) False
PA4376 pncB2 CDS None chromosome 4907841 4909037 + nicotinate phosphoribosyltransferase (NCBI) False
PA4400 PA4400 CDS None chromosome 4930748 4931695 - hypothetical protein (NCBI) False
PA4401 PA4401 CDS None chromosome 4931746 4932381 - probable glutathione S-transferase (NCBI) False
PA4642 PA4642 CDS None chromosome 5210706 5210996 - hypothetical protein (NCBI) False
PA4722 PA4722 CDS None chromosome 5301021 5302193 - hypothetical protein (NCBI) False
PA4731 panD CDS None chromosome 5313206 5313586 + aspartate 1-decarboxylase precursor (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.