Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 192 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 192

There are 12 regulatory influences for Module 192

Regulator Table (12)
Regulator Name Type
RSP_0443 tf
RSP_1606 tf
RSP_1231 tf
RSP_2888 tf
RSP_1776 tf
RSP_0728 tf
RSP_2850 tf
RSP_1704 tf
RSP_2922 tf
RSP_0611 tf
RSP_2494 tf
RSP_0394 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
8104 3.80e-02 CGGaAAaag
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8105 9.40e+00 TagAAgtCGcCCccaAaGaca
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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 192 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 3.68e-03 1.37e-02 11/26
Amino Acid Metabolism kegg subcategory 6.19e-04 4.50e-03 6/26
Glycine serine and threonine metabolism kegg pathway 1.04e-04 1.23e-03 3/26
Lysine biosynthesis kegg pathway 7.00e-06 1.38e-04 3/26
Global kegg category 1.10e-02 2.77e-02 9/26
Metabolism kegg subcategory 1.10e-02 2.77e-02 9/26
Metabolic pathways kegg pathway 7.03e-03 2.07e-02 9/26
Microbial metabolism in diverse environments kegg pathway 2.50e-03 1.09e-02 5/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA metabolism tigr mainrole 7.48e-04 1.28e-03 3/26
DNA replication, recombination, and repair tigr sub1role 5.10e-04 9.05e-04 3/26
Amino acid biosynthesis tigr mainrole 2.00e-06 5.00e-06 5/26
Aspartate family tigr sub1role 2.00e-06 4.00e-06 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 2.57e-02 3.94e-02 7/26
Translation, ribosomal structure and biogenesis cog subcategory 2.20e-02 3.41e-02 3/26
Cell wall/membrane/envelope biogenesis cog subcategory 2.63e-03 4.47e-03 4/26
Amino acid transport and metabolism cog subcategory 2.79e-02 4.26e-02 5/26
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 192

There are 26 genes in Module 192

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0366 RSP_0366 CDS None chromosome 1 2096173 2097465 - Adenylosuccinate synthetase (NCBI) False
RSP_0633 RSP_0633 CDS None chromosome 1 2369144 2370412 - UDP-N-acetylglucosamine enolpyruvyl transferase (NCBI) False
RSP_0687 RSP_0687 CDS None chromosome 1 2429936 2430649 + Predicted hydrolase (haloacid dehalogenase (HAD) superfamily) (NCBI) False
RSP_0725 RSP_0725 CDS None chromosome 1 2469725 2470276 - Thioredoxin, thioldisulfide interchange protein (NCBI) False
RSP_0744 RSP_0744 CDS None chromosome 1 2488629 2489216 - DNA-3-methyladenine glycosylase I (NCBI) False
RSP_0764 RSP_0764 CDS None chromosome 1 2506086 2507441 - Multi Antimicrobial Extrusion (MATE) family efflux pump NorM (NCBI) False
RSP_0832 RSP_0832 CDS None chromosome 1 2577892 2578989 + Putative GTP-binding protein (NCBI) False
RSP_0916 pmbA CDS None chromosome 1 2666209 2667552 + Putative PmbA/TldD protein invoved in modulation of DNA gyrase (NCBI) False
RSP_0934 gpmI CDS None chromosome 1 2683669 2685189 - Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent (NCBI) False
RSP_1068 argB CDS None chromosome 1 2825457 2826338 + acetylglutamate kinase (NCBI) False
RSP_1131 dapD CDS None chromosome 1 2894481 2895305 - 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI) False
RSP_1150 bacA CDS None chromosome 1 2914106 2914912 - Bacitracin Resistance Protein (NCBI) False
RSP_1151 RSP_1151 CDS None chromosome 1 2914945 2915931 - NADH-ubiquinone oxidoreductase (NCBI) False
RSP_1152 rnd CDS None chromosome 1 2916201 2916815 + Ribonuclease D (NCBI) False
RSP_1153 GutQ CDS None chromosome 1 2916838 2917761 + Sugar phosphate Isomerase (NCBI) False
RSP_1221 rph CDS None chromosome 1 2994260 2994985 + ribonuclease PH (NCBI) False
RSP_1222 ham1 CDS None chromosome 1 2994982 2995593 + putative Ham1p_like protein, Ham1 family (NCBI) False
RSP_1346 RSP_1346 CDS None chromosome 1 3115048 3117483 + DNA gyrase, subunit B (NCBI) False
RSP_1376 asd CDS None chromosome 1 3154962 3155984 + putative aspartate-semialdehyde dehydrogenase (NCBI) False
RSP_1390 RSP_1390 CDS None chromosome 1 3166804 3167685 + Putative transporter, DMT superfamily (NCBI) False
RSP_1580 lgt CDS None chromosome 1 172445 173323 - Prolipoprotein diacylglyceryl transferase (NCBI) False
RSP_1795 serS CDS None chromosome 1 380801 382093 - Probable Seryl-tRNA synthetase (NCBI) False
RSP_1831 thrC CDS None chromosome 1 422509 423894 + Threonine synthase (NCBI) False
RSP_2009 argF CDS None chromosome 1 610890 611816 + Aspartate/ornithine carbamoyltransferase (NCBI) False
RSP_2647 RSP_2647 CDS None chromosome 1 1290283 1291473 + Predicted SAM-dependent methyltransferases (NCBI) False
RSP_2968 RSP_2968 CDS None chromosome 1 1652437 1653843 - Probable dihydrolipoamide dehydrogenase (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 192

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.