Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 166 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 166

There are 13 regulatory influences for Module 166

Regulator Table (13)
Regulator Name Type
RSP_1739 tf
RSP_1231 tf
RSP_2889 tf
RSP_2494 tf
RSP_2730 tf
RSP_2922 tf
RSP_0698 tf
RSP_1163 tf
RSP_0394 tf
RSP_1704 tf
RSP_0755 tf
RSP_0395 tf
RSP_2850 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
8052 4.30e+00 TTtccCGC
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8053 4.70e+02 AATTCAGACCTTTTCCTGA
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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 166 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.18e-02 2.90e-02 10/26
Carbohydrate Metabolism kegg subcategory 3.29e-03 1.27e-02 5/26
Glycolysis / Gluconeogenesis kegg pathway 6.70e-05 8.66e-04 3/26
Pentose phosphate pathway kegg pathway 2.20e-05 3.51e-04 3/26
Energy Metabolism kegg subcategory 1.97e-04 2.01e-03 6/26
Carbon fixation in photosynthetic organisms kegg pathway 0.00e+00 0.00e+00 5/26
Genetic Information Processing kegg category 5.02e-03 1.67e-02 5/26
Translation kegg subcategory 1.84e-04 1.91e-03 5/26
Aminoacyl-tRNA biosynthesis kegg pathway 9.70e-05 1.17e-03 4/26
Global kegg category 1.10e-02 2.77e-02 9/26
Metabolism kegg subcategory 1.10e-02 2.77e-02 9/26
Metabolic pathways kegg pathway 7.03e-03 2.07e-02 9/26
Biosynthesis of secondary metabolites kegg pathway 2.54e-04 2.41e-03 7/26
Microbial metabolism in diverse environments kegg pathway 3.99e-04 3.28e-03 6/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
small_GTP tigrfam 1.00e-06 1.00e-06 3/26
Energy metabolism tigr mainrole 1.42e-02 1.72e-02 3/26
Protein synthesis tigr mainrole 6.56e-04 1.14e-03 4/26
tRNA aminoacylation tigr sub1role 1.60e-05 3.90e-05 3/26
Unknown function tigr mainrole 4.00e-05 9.00e-05 4/26
General tigr sub1role 6.00e-06 1.50e-05 4/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 2.64e-03 4.49e-03 8/26
Translation, ribosomal structure and biogenesis cog subcategory 1.00e-06 2.00e-06 8/26
Carbohydrate transport and metabolism cog subcategory 1.26e-02 2.02e-02 4/26
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 166

There are 26 genes in Module 166

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0005 guaA CDS None chromosome 1 1706705 1708261 + GMP synthase (glutamine-hydrolyzing) (NCBI) False
RSP_0385 RSP_0385 CDS None chromosome 1 2117070 2119010 + Threonyl-tRNA synthetase, class IIa (NCBI) False
RSP_0404 RSP_0404 CDS None chromosome 1 2136288 2137253 + fructose - 1,6 - bisphosphatase, GlpX-like (NCBI) False
RSP_0778 ProS CDS None chromosome 1 2520775 2522112 - Prolyl-tRNA synthetase, class IIa (NCBI) False
RSP_0815 aspS CDS None chromosome 1 2556582 2558357 - Aspartyl-tRNA synthetase (NCBI) False
RSP_0827 RSP_0827 CDS None chromosome 1 2571882 2572493 - Ribosomal protein L25 (NCBI) False
RSP_0832 RSP_0832 CDS None chromosome 1 2577892 2578989 + Putative GTP-binding protein (NCBI) False
RSP_0968 mdh CDS None chromosome 1 2730174 2731190 - malate dehydrogenase (RefSeq) False
RSP_1212 argG CDS None chromosome 1 2982879 2984105 + ArgG, Argininosuccinate synthase (NCBI) False
RSP_1376 asd CDS None chromosome 1 3154962 3155984 + putative aspartate-semialdehyde dehydrogenase (NCBI) False
RSP_1761 pheT CDS None chromosome 1 343336 345753 - Phenylalanyl-tRNA synthetase beta chain (NCBI) False
RSP_2088 lepA CDS None chromosome 1 681644 683443 - GTP-binding elongation factor (NCBI) False
RSP_2307 RSP_2307 CDS None chromosome 1 929740 930657 - probable manganese-dependent inorganic pyrophosphatase (NCBI) False
RSP_2453 RSP_2453 CDS None chromosome 1 1094553 1095218 - putative oxidoreductase (NAD/NADP dependent) (NCBI) False
RSP_2461 fabG CDS None chromosome 1 1102236 1102973 + 3-oxoacyl-(acyl-carrier protein) reductase (NCBI) False
RSP_2537 prfC CDS None chromosome 1 1180302 1181906 - Probable peptide chain release factor RF3 (NCBI) False
RSP_2697 RSP_2697 CDS None chromosome 1 1343517 1344164 + hypothetical protein (NCBI) False
RSP_2698 RSP_2698 CDS None chromosome 1 1344210 1345556 + putative quinoprotein (NCBI) False
RSP_2699 RSP_2699 CDS None chromosome 1 1345615 1347078 + Probable GTP-binding protein (NCBI) False
RSP_2737 RSP_2737 CDS None chromosome 1 1387180 1387527 - Putative ssRNA endoribonuclease L-PSP (NCBI) False
RSP_2956 tktA CDS None chromosome 1 1637358 1639376 + Transketolase (NCBI) False
RSP_3349 RSP_3349 CDS None chromosome 2 415224 416102 + hypothetical protein (NCBI) False
RSP_4042 RSP_4042 CDS None chromosome 1 1129054 1129647 + Peptidyl-prolyl cis-trans isomerase, cyclophilin type (NCBI) False
RSP_4043 RSP_4043 CDS None chromosome 1 1128555 1129064 + Peptidylprolyl isomerase (NCBI) False
RSP_4044 pgk CDS None chromosome 1 1127213 1128406 - Phosphoglycerate kinase (NCBI) False
RSP_4045 fbaB CDS None chromosome 1 1126182 1127111 - Fructose-bisphosphate aldolase class I (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 166

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.