Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 200 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 200

There are 10 regulatory influences for Module 200

Regulator Table (10)
Regulator Name Type
RSP_2410 tf
RSP_0087 tf
RSP_0698 tf
RSP_1231 tf
RSP_0032 tf
RSP_0327 tf
RSP_0394 tf
RSP_2425 tf
RSP_2610 tf
RSP_2853 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
8120 4.20e-03 gTcac..attt
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8121 1.20e-03 .TGCtGCattgcagcAtAc
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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 200 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 4.11e-03 6.88e-03 9/28
Cell wall/membrane/envelope biogenesis cog subcategory 5.30e-04 1.03e-03 5/28
Lipid transport and metabolism cog subcategory 1.36e-02 2.17e-02 3/28
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 200

There are 28 genes in Module 200

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0382 RSP_0382 CDS None chromosome 1 2112917 2114722 - poly-beta-hydroxybutyrate polymerase (NCBI) False
RSP_0383 RSP_0383 CDS None chromosome 1 2114824 2116095 + hypothetical protein (NCBI) False
RSP_0394 RSP_0394 CDS None chromosome 1 2123955 2124422 - hypothetical protein (NCBI) True
RSP_0600 RSP_0600 CDS None chromosome 1 2341664 2342491 - hypothetical protein (NCBI) False
RSP_0688 RSP_0688 CDS None chromosome 1 2430748 2432253 + Probable penicillin-binding protein (NCBI) False
RSP_0698 fnrL CDS None chromosome 1 2441421 2442167 - Crp-Fnr regulatory protein (FnrL) (NCBI) True
RSP_0959 RSP_0959 CDS None chromosome 1 2715617 2717317 - ATPase (NCBI) False
RSP_1022 RSP_1022 CDS None chromosome 1 2784615 2787392 - conserved hypothetical protein (possibly transmembrane) (NCBI) False
RSP_1023 RSP_1023 CDS None chromosome 1 2787392 2788264 - hypothetical protein (NCBI) False
RSP_1024 RSP_1024 CDS None chromosome 1 2788261 2789277 - Putative MoxR family protein (NCBI) False
RSP_1029 RSP_1029 CDS None chromosome 1 2793413 2793808 - possible Histidine triad (HIT) protein (NCBI) False
RSP_1109 cysK CDS None chromosome 1 2866248 2867324 + Cysteine synthase (NCBI) False
RSP_1199 RSP_1199 CDS None chromosome 1 2969569 2970171 - secreted conserved hypothetical protein (NCBI) False
RSP_2261 ydjI CDS None chromosome 1 878349 879458 - Antifreeze protein, type I (NCBI) False
RSP_2344 fabI1 CDS None chromosome 1 969700 970524 - enoyl-acyl carrier protein reductase (NCBI) False
RSP_2410 rpoH1 CDS None chromosome 1 1039301 1040197 + sigma factor RpoH1 (Sigma-32 group, heat shock) (NCBI) True
RSP_2550 exoK CDS None chromosome 1 1193730 1194512 - endo-beta-1,3-1,4-glycanase protein (NCBI) False
RSP_2561 exoP CDS None chromosome 1 1204993 1207308 - putative succinoglycan biosynthesis transport protein ExoP (NCBI) False
RSP_2562 exoM CDS None chromosome 1 1207359 1208339 - succinoglycan biosynthesis protein exoM (NCBI) False
RSP_2563 exoA CDS None chromosome 1 1208336 1209325 - Glycosyl transferase, family 2 (NCBI) False
RSP_2564 exoL CDS None chromosome 1 1209322 1210491 - glycosyltransferase, Succinoglycan biosynthesis protein exoL (NCBI) False
RSP_2565 ugpG CDS None chromosome 1 1210513 1211451 - UDPG-pyrophosphorylase (NCBI) False
RSP_2639 RSP_2639 CDS None chromosome 1 1280450 1281292 - Putative arginine-tRNA protein transferase (NCBI) False
RSP_2806 lon CDS None chromosome 1 1508872 1511280 - Probable ATP-dependent protease La protein (NCBI) False
RSP_3229 RSP_3229 CDS None chromosome 2 287499 288887 - Membrane-bound lytic murein transglycosylase B (NCBI) False
RSP_3597 RSP_3597 CDS None chromosome 2 690311 691258 - CorC/Hlyc family protein with CBS domains (NCBI) False
RSP_3598 RSP_3598 CDS None chromosome 2 691298 691801 - Protein of unknown function UPF0054 (NCBI) False
RSP_3599 RSP_3599 CDS None chromosome 2 691785 692825 - 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 200

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.