Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 209 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 209

There are 11 regulatory influences for Module 209

Regulator Table (11)
Regulator Name Type
RSP_0623 tf
RSP_1866 tf
RSP_1164 tf
RSP_0547 tf
RSP_1220 tf
RSP_3202 tf
RSP_2324 tf
RSP_1191 tf
RSP_0395 tf
RSP_0386 tf
RSP_1892 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
8138 2.20e-06 AAcAa.AcTATA.TCtgT
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8139 5.20e+00 aaAtaGGCGaacaTGaCtCGGACG
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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 209 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Nucleotide Metabolism kegg subcategory 5.18e-03 1.70e-02 3/29
Folding Sorting and Degradation kegg subcategory 3.15e-04 2.77e-03 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 1.98e-02 3.09e-02 7/29
Translation, ribosomal structure and biogenesis cog subcategory 1.08e-03 1.96e-03 5/29
Replication, recombination and repair cog subcategory 1.53e-03 2.69e-03 4/29
Defense mechanisms cog subcategory 8.10e-05 2.02e-04 3/29
Nucleotide transport and metabolism cog subcategory 2.42e-03 4.13e-03 3/29
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 209

There are 29 genes in Module 209

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0448 RSP_0448 CDS None chromosome 1 2178615 2180435 + EF-Tu; elongation factor Tu (NCBI) False
RSP_0684 RSP_0684 CDS None chromosome 1 2427604 2428413 - Possible oxidoreductase; Short-chain dehydrogenase/reductase SDR (NCBI) False
RSP_0685 RSP_0685 CDS None chromosome 1 2428426 2429427 - Possible ribosomal RNA small subunit methyltransferase C RsmC (NCBI) False
RSP_0686 RSP_0686 CDS None chromosome 1 2429444 2429764 - ATP-dependent Clp protease adaptor protein clpS (NCBI) False
RSP_0687 RSP_0687 CDS None chromosome 1 2429936 2430649 + Predicted hydrolase (haloacid dehalogenase (HAD) superfamily) (NCBI) False
RSP_0818 carB CDS None chromosome 1 2560488 2563829 + carbamoyl phosphate synthase large subunit (RefSeq) False
RSP_0819 rhlE2 CDS None chromosome 1 2564430 2565815 + DEAD/DEAH box helicase (NCBI) False
RSP_1062 RSP_1062 CDS None chromosome 1 2818740 2819618 + ATPases of the PP superfamily (NCBI) False
RSP_1065 RSP_1065 CDS None chromosome 1 2823196 2823939 + hypothetical protein (NCBI) False
RSP_1075 RSP_1075 CDS None chromosome 1 2831175 2831975 - Short-chain dehydrogenase/reductase SDR (NCBI) False
RSP_1108 TruB CDS None chromosome 1 2865122 2866027 + tRNA pseudouridine synthase B (NCBI) False
RSP_1110 RSP_1110 CDS None chromosome 1 2867723 2868235 + hypothetical protein (NCBI) False
RSP_1197 HemH CDS None chromosome 1 2967945 2969078 + Ferrochelatase (NCBI) False
RSP_1202 TrmA CDS None chromosome 1 2971536 2972750 - putative RNA SAM-dependent methyltransferase, TrmA family (NCBI) False
RSP_1203 RSP_1203 CDS None chromosome 1 2972747 2974591 - ABC multidrug efflux pump, fused ATPase and inner membrane subunits (NCBI) False
RSP_1218 mutS CDS None chromosome 1 2989762 2992389 + DNA mismatch repair protein MutS (NCBI) False
RSP_1426 RSP_1426 CDS None chromosome 1 5531 6823 - RNA-binding region RNP-1 (NCBI) False
RSP_1427 RSP_1427 CDS None chromosome 1 6925 7335 + hypothetical protein (NCBI) False
RSP_1484 RSP_1484 CDS None chromosome 1 70003 70527 - hypothetical protein (NCBI) False
RSP_1485 RSP_1485 CDS None chromosome 1 70529 72337 - ATP-dependent RNA helicase (NCBI) False
RSP_1799 secF CDS None chromosome 1 385065 386039 + protein-export membrane protein SecF (NCBI) False
RSP_1970 RSP_1970 CDS None chromosome 1 561822 562370 + Phosphoribosylglycinamide formyltransferase (NCBI) False
RSP_2118 recN CDS None chromosome 1 718756 720396 + DNA repair protein RecN (NCBI) False
RSP_2552 exoU CDS None chromosome 1 1196164 1197120 - Glycosyl transferase, family 2 (NCBI) False
RSP_2648 RSP_2648 CDS None chromosome 1 1291470 1292012 + hypothetical protein (NCBI) False
RSP_3004 RSP_3004 CDS None chromosome 2 39958 40566 + Possible Protein kinase (NCBI) False
RSP_3273 RSP_3273 CDS None chromosome 2 331964 332725 - ABC multidrug/carbohydrate efflux transporter, inner membrane subunit (NCBI) False
RSP_3274 RSP_3274 CDS None chromosome 2 332722 333648 - ABC multidrug/carbohydrate efflux transporter, ATPase subunit (NCBI) False
RSP_3591 RSP_3591 CDS None chromosome 2 683499 684119 - cytidylate kinase (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 209

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.