Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 66 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 66

There are 7 regulatory influences for Module 66

Regulator Table (7)
Regulator Name Type
RSP_2200 tf
RSP_0402 tf
RSP_2591 tf
RSP_0755 tf
RSP_1518 tf
RSP_2963 tf
RSP_2950 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
7852 1.00e+00 Ttacg.agCGT
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7853 1.60e+03 CctCgtcactGgcCGGcacGAt
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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 66 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.80e-05 2.99e-04 13/22
Carbohydrate Metabolism kegg subcategory 1.30e-03 7.29e-03 5/22
Propanoate metabolism kegg pathway 2.00e-05 3.21e-04 3/22
Butanoate metabolism kegg pathway 0.00e+00 3.00e-06 5/22
Lipid Metabolism kegg subcategory 2.00e-06 5.10e-05 5/22
Fatty acid metabolism kegg pathway 0.00e+00 6.00e-06 4/22
Synthesis and degradation of ketone bodies kegg pathway 0.00e+00 1.00e-06 3/22
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 10/22
Valine leucine and isoleucine degradation kegg pathway 0.00e+00 0.00e+00 10/22
Lysine degradation kegg pathway 4.00e-06 7.70e-05 3/22
Tryptophan metabolism kegg pathway 7.00e-06 1.27e-04 3/22
Metabolism of Terpenoids and Polyketides kegg subcategory 0.00e+00 0.00e+00 7/22
Geraniol degradation kegg pathway 0.00e+00 0.00e+00 5/22
Xenobiotics Biodegradation and Metabolism kegg subcategory 0.00e+00 1.00e-06 6/22
Benzoate degradation kegg pathway 1.00e-06 2.70e-05 3/22
Naphthalene degradation kegg pathway 0.00e+00 5.00e-06 3/22
Global kegg category 3.00e-06 5.60e-05 13/22
Metabolism kegg subcategory 3.00e-06 5.60e-05 13/22
Metabolic pathways kegg pathway 3.43e-04 2.93e-03 10/22
Biosynthesis of secondary metabolites kegg pathway 7.00e-06 1.38e-04 8/22
Microbial metabolism in diverse environments kegg pathway 1.25e-04 1.42e-03 6/22

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 5.00e-06 2.00e-05 17/22
Lipid transport and metabolism cog subcategory 0.00e+00 0.00e+00 14/22
Secondary metabolites biosynthesis, transport and catabolism cog subcategory 1.68e-03 2.94e-03 3/22
Acyl-CoA dehydrogenases cog 0.00e+00 0.00e+00 5/22
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 66

There are 22 genes in Module 66

Gene Member Table (22)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0154 RSP_0154 CDS None chromosome 1 1868401 1869273 - 3-hydroxyisobutyrate dehydrogenase (NCBI) False
RSP_0155 RSP_0155 CDS None chromosome 1 1869270 1870301 - enoyl-CoA hydratase (NCBI) False
RSP_0156 RSP_0156 CDS None chromosome 1 1870298 1871437 - Acyl-CoA dehydrogenase (NCBI) False
RSP_0741 RSP_0741 CDS None chromosome 1 2484712 2485746 - putative metallo-beta-lactamase family protein (NCBI) False
RSP_0742 RSP_0742 CDS None chromosome 1 2485743 2487431 - probable acyl-CoA dehydrogenase (NCBI) False
RSP_1252 RSP_1252 CDS None chromosome 1 3020270 3021211 - 2-nitropropane dioxygenase-like protein (NCBI) False
RSP_1354 RSP_1354 CDS None chromosome 1 3124864 3126033 + Thiolase (NCBI) False
RSP_2198 RSP_2198 CDS None chromosome 1 812885 813328 - hypothetical protein (NCBI) False
RSP_2199 RSP_2199 CDS None chromosome 1 813355 815130 - putative acyl-CoA dehydrogenase (NCBI) False
RSP_2200 RSP_2200 CDS None chromosome 1 815149 815547 - transcriptional regulator, MerR family (NCBI) True
RSP_2255 RSP_2255 CDS None chromosome 1 872149 874038 + Long-chain-fatty-acid--CoA ligase (NCBI) False
RSP_2506 ivdH CDS None chromosome 1 1150728 1151885 + Isovaleryl-CoA dehydrogenase (NCBI) False
RSP_2508 mccB CDS None chromosome 1 1152653 1154329 + Methylcrotonyl-CoA carboxylase beta chain (NCBI) False
RSP_2509 mccA CDS None chromosome 1 1154426 1156366 + Methylcrotonyl-CoA carboxylase alpha chain (NCBI) False
RSP_2510 hmgL CDS None chromosome 1 1156359 1157243 + Hydroxymethylglutaryl-CoA lyase (NCBI) False
RSP_2511 RSP_2511 CDS None chromosome 1 1157256 1158044 + enoyl-CoA hydratase/isomerase family protein (NCBI) False
RSP_2635 RSP_2635 DUMMY None chromosome 1 0 0 + None False
RSP_2655 RSP_2655 CDS None chromosome 1 1298787 1299185 - hypothetical protein (NCBI) False
RSP_3181 RSP_3181 CDS None chromosome 2 232784 233965 - putative fatty-acyl-CoA racemase; CoA-transferase family III (NCBI) False
RSP_3182 RSP_3182 CDS None chromosome 2 233962 235095 - Acyl-CoA dehydrogenase (NCBI) False
RSP_3183 RSP_3183 CDS None chromosome 2 235092 235853 - 3-hydroxyacyl-CoA dehydrogenase type II (NCBI) False
RSP_3184 RSP_3184 CDS None chromosome 2 235853 237013 - putative Thiolase (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 66

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.