Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 108 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 108

There are 14 regulatory influences for Module 108

Regulator Table (14)
Regulator Name Type
RSP_1231 tf
RSP_2963 tf
RSP_2410 tf
RSP_2494 tf
RSP_3322 tf
RSP_1741 tf
RSP_2888 tf
RSP_1776 tf
RSP_1607 tf
RSP_3505 tf
RSP_1871 tf
RSP_1590 tf
RSP_2027 tf
RSP_0087 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
7936 1.30e+00 TTtG.GtTTcgcGaa
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7937 6.80e-01 aAa..atcaaAGATCaggacgaAA
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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 108 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 5.38e-03 1.74e-02 11/27
Metabolism of Cofactors and Vitamins kegg subcategory 1.82e-02 3.92e-02 3/27
Ubiquinone and other terpenoid-quinone biosynthesis kegg pathway 0.00e+00 4.00e-06 3/27
Global kegg category 1.29e-03 7.26e-03 11/27
Metabolism kegg subcategory 1.29e-03 7.26e-03 11/27
Metabolic pathways kegg pathway 9.52e-03 2.51e-02 9/27
Biosynthesis of secondary metabolites kegg pathway 3.39e-04 2.91e-03 7/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 5.79e-04 1.01e-03 4/27
Menaquinone and ubiquinone tigr sub1role 0.00e+00 0.00e+00 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.91e-03 3.31e-03 16/27
Coenzyme transport and metabolism cog subcategory 3.31e-03 5.60e-03 4/27
Lipid transport and metabolism cog subcategory 1.82e-03 3.16e-03 4/27
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 108

There are 27 genes in Module 108

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0146 glnB CDS None chromosome 1 1859643 1859981 + Nitrogen regulatory protein P-II (NCBI) False
RSP_0230 RSP_0230 CDS None chromosome 1 1948474 1950069 - Neutral zinc metallopeptidase (NCBI) False
RSP_0352 RSP_0352 CDS None chromosome 1 2083151 2083474 - probable ferredoxin (NCBI) False
RSP_0565 RSP_0565 CDS None chromosome 1 2302340 2303056 + putative phosphatidylcholine synthase (NCBI) False
RSP_0571 RSP_0571 CDS None chromosome 1 2310595 2311362 + tRNA pseudouridine synthase (NCBI) False
RSP_0662 RSP_0662 CDS None chromosome 1 2402130 2402447 - Putative chorismate mutase (NCBI) False
RSP_0812 RSP_0812 CDS None chromosome 1 2554340 2554744 - Glyoxalase I (lactoylglutathione lyase) (NCBI) False
RSP_1027 RSP_1027 CDS None chromosome 1 2790207 2790425 + hypothetical protein (NCBI) False
RSP_1134 Dxs CDS None chromosome 1 2896821 2898734 - 1 deoxyxylulose-5-phosphate synthase (NCBI) False
RSP_1135 ispA CDS None chromosome 1 2898744 2899613 - geranylgeranyl pyrophosphate synthetase (NCBI) False
RSP_1136 xseB CDS None chromosome 1 2899610 2899849 - exonuclease VII small subunit (NCBI) False
RSP_1137 RSP_1137 CDS None chromosome 1 2899846 2900769 - Histone deacetylase family protein (NCBI) False
RSP_1175 ubiG CDS None chromosome 1 2942900 2943643 + 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4 benzoquinol methylase (NCBI) False
RSP_1232 RSP_1232 CDS None chromosome 1 3004389 3004886 - putative integral membrane protein (NCBI) False
RSP_1254 RSP_1254 CDS None chromosome 1 3021856 3023046 - putative acetate kinase (acetokinase (NCBI) False
RSP_1337 aarF CDS None chromosome 1 3105782 3107263 - probable ubiquinone biosynthesis protein (NCBI) False
RSP_1338 ubiE CDS None chromosome 1 3107313 3108065 - methyltransferase (NCBI) False
RSP_1571 purE CDS None chromosome 1 164159 164644 - Phosphoribosylaminoimidazole carboxylase, catalytic subunit (NCBI) False
RSP_1628 RSP_1628 CDS None chromosome 1 224676 225674 + possible sensor histidine protein kinase (NCBI) False
RSP_1629 RSP_1629 CDS None chromosome 1 225687 226076 + response regulator receiver domain protein (NCBI) False
RSP_2249 RSP_2249 CDS None chromosome 1 865112 866332 - multidrug (Tetracycline) efflux pump, Major facilitator superfamily (MFS) (NCBI) False
RSP_2787 RSP_2787 CDS None chromosome 1 1434468 1434920 + hypothetical protein (NCBI) False
RSP_2983 RSP_2983 CDS None chromosome 1 1673427 1674554 - hypothetical protein (NCBI) False
RSP_3003 RSP_3003 CDS None chromosome 2 39397 39693 + hypothetical protein (NCBI) False
RSP_3090 phnA CDS None chromosome 2 135194 135523 + Putative alkylphosphonate uptake protein, phnA (NCBI) False
RSP_3176 fabI CDS None chromosome 2 228690 229478 - enoyl-(acyl-carrier protein) reductase (NADH) (NCBI) False
RSP_3835 RSP_3835 CDS None chromosome 2 30711 31070 - 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 108

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.