Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 323 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 323

There are 10 regulatory influences for Module 323

Regulator Table (10)
Regulator Name Type
RSP_3124 tf
RSP_3731 tf
RSP_1776 tf
RSP_2850 tf
RSP_0032 tf
RSP_1936 tf
RSP_1785 tf
RSP_1286 tf
RSP_3022 tf
RSP_2610 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
8356 4.50e-08 aaaaAttttc.t.tGaTttTCa.t
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8357 2.50e+01 aaagtaaacGaTaTtgATaaT
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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 323 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 6.38e-03 1.95e-02 5/29
Arginine and proline metabolism kegg pathway 3.15e-04 2.77e-03 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 1.58e-02 2.50e-02 4/29
Amino acid transport and metabolism cog subcategory 1.41e-02 2.24e-02 6/29
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 323

There are 29 genes in Module 323

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0008 RSP_0008 CDS None chromosome 1 1710871 1711836 + possible transporter, DME family, DMT superfamily (NCBI) False
RSP_0214 RSP_0214 CDS None chromosome 1 1927099 1927404 - possible uncharacterized phage protein (NCBI) False
RSP_0393 RSP_0393 CDS None chromosome 1 2122870 2123940 - probable riboflavin biosynthesis protein (NCBI) False
RSP_0563 RSP_0563 CDS None chromosome 1 2300496 2301416 + putative site-specific recombinase (NCBI) False
RSP_0824 pth CDS None chromosome 1 2570458 2571135 - Peptidyl-tRNA hydrolase (NCBI) False
RSP_0953 RSP_0953 CDS None chromosome 1 2705867 2708251 - hypothetical protein (NCBI) False
RSP_1022 RSP_1022 CDS None chromosome 1 2784615 2787392 - conserved hypothetical protein (possibly transmembrane) (NCBI) False
RSP_1174 pip CDS None chromosome 1 2941873 2942838 - Prolyl aminopeptidase (NCBI) False
RSP_1365 RSP_1365 CDS None chromosome 1 3143461 3144087 + hypothetical protein (NCBI) False
RSP_1384 RSP_1384 CDS None chromosome 1 3162861 3163850 + hypothetical protein (NCBI) False
RSP_1474 nspC CDS None chromosome 1 58616 59713 + putative carboxynorspermidine decarboxylase protein (NCBI) False
RSP_1780 RSP_1780 CDS None chromosome 1 365227 365712 + hypothetical protein (NCBI) False
RSP_1894 RSP_1894 CDS None chromosome 1 490925 491314 + hypothetical protein (NCBI) False
RSP_1924 RSP_1924 CDS None chromosome 1 521753 522190 - BioY family protein (NCBI) False
RSP_1993 RSP_1993 CDS None chromosome 1 590153 590629 - hypothetical protein (NCBI) False
RSP_2005 ybaU CDS None chromosome 1 604158 606023 - possible peptidyl-prolyl cis-trans isomerse (NCBI) False
RSP_2018 RSP_2018 CDS None chromosome 1 619783 620094 - hypothetical protein (NCBI) False
RSP_2215 RSP_2215 CDS None chromosome 1 827623 828027 - hypothetical protein (NCBI) False
RSP_2557 asnB CDS None chromosome 1 1199579 1201459 + putative asparagine synthetase (NCBI) False
RSP_2746 RSP_2746 CDS None chromosome 1 1395862 1396806 - hypothetical protein (NCBI) False
RSP_2946 argC CDS None chromosome 1 1626093 1627121 - N-acetyl-gamma-glutamyl-phosphate reductase (NCBI) False
RSP_3022 RSP_3022 CDS None chromosome 2 53250 53951 + transcriptional regulator, TetR family (NCBI) True
RSP_3094 RSP_3094 CDS None chromosome 2 137758 138525 - Putative transmembrane anti-sigma factor (NCBI) True
RSP_3124 RSP_3124 CDS None chromosome 2 169000 169896 + transcriptional regulator, LysR family (NCBI) True
RSP_3125 RSP_3125 CDS None chromosome 2 169950 170282 + transcriptional regulator, ArsR familyy (NCBI) True
RSP_3422 RSP_3422 CDS None chromosome 2 490715 491281 + hypothetical protein (NCBI) False
RSP_3592 aroA CDS None chromosome 2 684191 685528 - EPSP synthase, 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI) False
RSP_3675 RSP_3675 CDS None chromosome 2 794257 795174 - Esterase/lipase/thioesterase (NCBI) False
RSP_3677 RSP_3677 CDS None chromosome 2 796023 797102 + ABC sugar transporter, ATPase subunit (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 323

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.