Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 84 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 84

There are 5 regulatory influences for Module 84

Regulator Table (5)
Regulator Name Type
RSP_1660 tf
RSP_3341 tf
RSP_0755 tf
RSP_0386 tf
RSP_3238 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
7888 1.20e-01 aGAtCGgTCAgCTtccGccCCcG
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7889 9.10e+00 CcgAAGGcTcG.aacaaccCGCGg
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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 84 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Environmental Information Processing kegg category 2.75e-03 1.14e-02 6/25
Signal Transduction kegg subcategory 2.00e-06 3.90e-05 6/25
Two-component system kegg pathway 2.00e-06 3.90e-05 6/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 2.15e-03 3.28e-03 3/25
Cations and iron carrying compounds tigr sub1role 3.00e-06 8.00e-06 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 7.76e-03 1.27e-02 7/25
Replication, recombination and repair cog subcategory 6.10e-03 1.01e-02 3/25
Signal transduction mechanisms cog subcategory 1.85e-02 2.89e-02 3/25
Cell wall/membrane/envelope biogenesis cog subcategory 1.39e-02 2.21e-02 3/25
Inorganic ion transport and metabolism cog subcategory 2.82e-02 4.30e-02 3/25
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 84

There are 25 genes in Module 84

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0923 map1 CDS None chromosome 1 2672577 2673458 - Methionine aminopeptidase, subfamily 1 (NCBI) False
RSP_0925 yobR CDS None chromosome 1 2674268 2674978 + Putative acetyl transferase (NCBI) False
RSP_0926 RSP_0926 CDS None chromosome 1 2674975 2675907 + OmpA/MotB family protein (NCBI) False
RSP_0987 RSP_0987 CDS None chromosome 1 2744222 2745178 + Putative transporter, RarD family, DMT superfamily (NCBI) False
RSP_1263 RSP_1263 CDS None chromosome 1 3030317 3030877 - hypothetical protein (NCBI) False
RSP_1264 RSP_1264 CDS None chromosome 1 3031106 3031192 + hypothetical protein (NCBI) False
RSP_1265 kdpA CDS None chromosome 1 3031200 3032855 + Potassium-transporting P-type ATPase, A chain, KdpA (NCBI) False
RSP_1266 kdpB CDS None chromosome 1 3032864 3034891 + Potassium-transporting P-type ATPase, B chain, KdpB (NCBI) False
RSP_1267 kdpC CDS None chromosome 1 3034904 3035461 + Potassium-transporting P-type ATPase C chain, kdpC (NCBI) False
RSP_1268 kdpD CDS None chromosome 1 3035465 3038128 + Osmosensitive K+ channel histidine kinase (NCBI) False
RSP_1269 kdpE CDS None chromosome 1 3038125 3038811 + two component transcriptional regulator, winged helix family (NCBI) False
RSP_1339 RSP_1339 CDS None chromosome 1 3108159 3109010 + Formamidopyrimidine-DNA glycolase (NCBI) False
RSP_1462 lpxK CDS None chromosome 1 47999 48997 + Putative Tetraacyldisaccharide-1-P 4'-kinase (NCBI) False
RSP_1470 rnhB CDS None chromosome 1 55434 56072 - ribonuclease HII (NCBI) False
RSP_1970 RSP_1970 CDS None chromosome 1 561822 562370 + Phosphoribosylglycinamide formyltransferase (NCBI) False
RSP_2534 RSP_2534 CDS None chromosome 1 1176049 1177722 + Predicted hydrolase of the metallo-beta-lactamase superfamily (NCBI) False
RSP_2599 phoB CDS None chromosome 1 1240670 1241362 - Phosphate regulon transcriptional regulator, PhoR (NCBI) False
RSP_2790 RSP_2790 CDS None chromosome 1 1532219 1532440 + hypothetical protein (NCBI) False
RSP_2815 xerD CDS None chromosome 1 1497308 1498243 + Probable integrase/recombinase XerD (NCBI) False
RSP_2818 aroB CDS None chromosome 1 1493773 1494885 - Putative 3-dehydroquinate synthase (NCBI) False
RSP_3091 RSP_3091 CDS None chromosome 2 135587 136183 - Coserved hypothetical protein (NCBI) False
RSP_3448 RSP_3448 CDS None chromosome 2 518535 519203 - transcriptional regulator, GntR-family (NCBI) True
RSP_3449 RSP_3449 CDS None chromosome 2 519194 520258 - Putative allophanate hydrolase subunit 2 (NCBI) False
RSP_3450 RSP_3450 CDS None chromosome 2 520255 520992 - hypothetical protein (NCBI) False
RSP_3565 RSP_3565 CDS None chromosome 2 660348 661139 + Glycoside hydrolase, family 25 (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 84

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.