Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 216 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 216

There are 13 regulatory influences for Module 216

Regulator Table (13)
Regulator Name Type
RSP_2200 tf
RSP_0601 tf
RSP_0032 tf
RSP_3094 tf
RSP_2130 tf
RSP_3686 tf
RSP_2236 tf
RSP_2171 tf
RSP_0794 tf
RSP_1220 tf
RSP_3665 tf
RSP_2838 tf
RSP_0999 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
8152 1.10e+00 aTcGA.aAG.T
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8153 3.90e+03 AtGATCaCGat
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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 216 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 1.85e-04 1.91e-03 7/29
Glyoxylate and dicarboxylate metabolism kegg pathway 0.00e+00 1.30e-05 5/29
Energy Metabolism kegg subcategory 4.12e-04 3.35e-03 6/29
Methane metabolism kegg pathway 5.00e-06 1.07e-04 4/29
Microbial metabolism in diverse environments kegg pathway 8.20e-04 5.42e-03 6/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 1.53e-03 2.69e-03 4/29
Energy production and conversion cog subcategory 5.73e-03 9.50e-03 5/29
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 216

There are 29 genes in Module 216

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0351 RSP_0351 CDS None chromosome 1 2081929 2082993 + D-threo-aldose 1-dehydrogenase (NCBI) False
RSP_0408 RSP_0408 CDS None chromosome 1 2141667 2142605 + hypothetical protein (NCBI) False
RSP_0424 RSP_0424 CDS None chromosome 1 2155955 2156563 + hypothetical protein (NCBI) False
RSP_0559 msrA CDS None chromosome 1 2295945 2296619 - Peptide methionine sulfoxide reductase (NCBI) False
RSP_0608 RSP_0608 CDS None chromosome 1 2349051 2349434 - hypothetical protein (NCBI) False
RSP_0716 RSP_0716 CDS None chromosome 1 2462206 2463192 - NADPH/quinone reductase and related Zn-dependent oxidoreductases (NCBI) False
RSP_1058 RSP_1058 CDS None chromosome 1 2816983 2817711 - hypothetical transmemebrane protein (NCBI) False
RSP_1076 sohB CDS None chromosome 1 2832130 2832927 - Peptidase family S49 (NCBI) False
RSP_1077 RSP_1077 CDS None chromosome 1 2833404 2834294 + transcriptional regulator, LysR family (NCBI) True
RSP_1078 fdsG CDS None chromosome 1 2834395 2834868 + NAD-dependent formate dehydrogenase, gamma subunit (24 kDa) (NCBI) False
RSP_1079 fdsB CDS None chromosome 1 2834865 2836394 + NAD dependent formate dehydrogenase, beta subunit (51 kDa) (NCBI) False
RSP_1080 fdsA CDS None chromosome 1 2836391 2839273 + NAD-dependent formate dehydrogenase, alpha subunit (NCBI) False
RSP_1081 fdsC CDS None chromosome 1 2839270 2840085 + formate dehydrogenase chain C (NCBI) False
RSP_1082 fdsD CDS None chromosome 1 2840075 2840296 + NAD-dependent formate dehydrogenase, delta subunit (NCBI) False
RSP_1204 RSP_1204 CDS None chromosome 1 2974588 2976432 - ABC multidrug efflux pump, fused ATPase and inner membrane subunits (NCBI) False
RSP_1220 hrcA CDS None chromosome 1 2993068 2994138 - heat-inducible transcription repressor HrcA (NCBI) True
RSP_1408 clpB CDS None chromosome 1 3183269 3185881 + Chaperone ClpB (NCBI) False
RSP_1743 RSP_1743 CDS None chromosome 1 324610 325923 + ATPase, AAA family (NCBI) False
RSP_1873 RSP_1873 CDS None chromosome 1 471693 472574 - hypothetical protein (NCBI) False
RSP_2121 RSP_2121 CDS None chromosome 1 722305 722934 - hypothetical protein (NCBI) False
RSP_2196 RSP_2196 CDS None chromosome 1 809387 811588 - enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxybutyryl-CoA epimerase (NCBI) False
RSP_2197 RSP_2197 CDS None chromosome 1 811603 812814 - Acetoacetyl-CoA thiolase (NCBI) False
RSP_2638 RSP_2638 CDS None chromosome 1 1279043 1279960 - putative sodium/calcium exchanger (NCBI) False
RSP_2640 RSP_2640 CDS None chromosome 1 1281399 1281851 - hypothetical protein (NCBI) False
RSP_2966 uvrA CDS None chromosome 1 1648123 1650981 - ABC excinuclease subunit A (NCBI) False
RSP_3377 RSP_3377 CDS None chromosome 2 441633 442517 + Glutathione S-transferase family protein (NCBI) False
RSP_3602 RSP_3602 CDS None chromosome 2 695125 695814 + ABC efflux transporter, ATPase subunit (NCBI) False
RSP_3603 RSP_3603 CDS None chromosome 2 695811 698318 + Possible ABC efflux tranporter, fused inner membrane domains (NCBI) False
RSP_3686 RSP_3686 CDS None chromosome 2 807600 808640 + transcriptional regulator, LacI family (NCBI) True

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 216

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.