Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 360 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 360

There are 11 regulatory influences for Module 360

Regulator Table (11)
Regulator Name Type
RSP_1231 tf
RSP_0728 tf
RSP_1704 tf
RSP_2610 tf
RSP_1077 tf
RSP_2494 tf
RSP_2130 tf
RSP_1925 tf
RSP_1014 tf
RSP_3684 tf
RSP_3700 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
8418 4.10e-02 tTttggCaaGAtcgc
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8419 5.00e+02 AAATtCAA
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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 360 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 6.19e-04 4.50e-03 12/25
Energy Metabolism kegg subcategory 6.78e-03 2.02e-02 4/25
Lipid Metabolism kegg subcategory 1.12e-03 6.66e-03 3/25
Fatty acid biosynthesis kegg pathway 8.00e-06 1.43e-04 3/25
Amino Acid Metabolism kegg subcategory 2.91e-03 1.19e-02 5/25
Genetic Information Processing kegg category 4.08e-03 1.46e-02 5/25
Translation kegg subcategory 9.35e-03 2.48e-02 3/25
Aminoacyl-tRNA biosynthesis kegg pathway 1.06e-03 6.45e-03 3/25
Global kegg category 5.47e-04 4.11e-03 11/25
Metabolism kegg subcategory 5.47e-04 4.11e-03 11/25
Metabolic pathways kegg pathway 2.99e-04 2.68e-03 11/25
Microbial metabolism in diverse environments kegg pathway 2.01e-03 9.58e-03 5/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 1.23e-02 1.52e-02 3/25
Protein synthesis tigr mainrole 5.42e-04 9.58e-04 4/25
tRNA aminoacylation tigr sub1role 1.40e-05 3.40e-05 3/25
Protein fate tigr mainrole 6.90e-05 1.44e-04 4/25
Protein and peptide secretion and trafficking tigr sub1role 1.60e-05 3.90e-05 3/25
Amino acid biosynthesis tigr mainrole 4.98e-04 8.95e-04 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 3.35e-03 5.65e-03 4/25
Cell wall/membrane/envelope biogenesis cog subcategory 1.39e-02 2.21e-02 3/25
Coenzyme transport and metabolism cog subcategory 1.45e-02 2.31e-02 3/25
Lipid transport and metabolism cog subcategory 9.11e-03 1.48e-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 360

There are 25 genes in Module 360

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0367 RSP_0367 CDS None chromosome 1 2097776 2098402 + Preprotein translocase SecG subunit (NCBI) False
RSP_0385 RSP_0385 CDS None chromosome 1 2117070 2119010 + Threonyl-tRNA synthetase, class IIa (NCBI) False
RSP_0444 RSP_0444 CDS None chromosome 1 2175063 2175722 + hypothetical protein (NCBI) False
RSP_0587 RSP_0587 CDS None chromosome 1 2329855 2331510 + Putative ABC transporter, fused ATPase subunits (NCBI) False
RSP_0929 accD CDS None chromosome 1 2678351 2679304 + Acetyl-CoA carboxylase carboxyl transferase, beta subunit (NCBI) False
RSP_1351 serC CDS None chromosome 1 3121118 3122275 + phosphoserine aminotransferase (NCBI) False
RSP_1352 RSP_1352 CDS None chromosome 1 3122347 3123951 + D-3-phosphoglycerate dehydrogenase (NCBI) False
RSP_1494 RSP_1494 CDS None chromosome 1 79022 80200 + putative aspartate aminotransferase (NCBI) False
RSP_1495 RSP_1495 CDS None chromosome 1 80211 83495 + Putative cell division protein (NCBI) False
RSP_1514 ahcY CDS None chromosome 1 100961 102352 - Adenosylhomocysteinase (NCBI) False
RSP_1519 prrC CDS None chromosome 1 105121 105816 - PrrC (NCBI) False
RSP_1674 RSP_1674 CDS None chromosome 1 264610 265449 + type 1 signal peptidase (NCBI) False
RSP_1763 pheS CDS None chromosome 1 346893 347975 - Phenylalanyl-tRNA synthetase alpha subunit (NCBI) False
RSP_1808 trpS CDS None chromosome 1 394430 395503 - tryptophanyl-tRNA synthetase (NCBI) False
RSP_1851 metZ CDS None chromosome 1 445037 446251 + O-succinylhomoserine sulfhydrylase (NCBI) False
RSP_2126 purC CDS None chromosome 1 726902 727654 + SAICAR synthetase (NCBI) False
RSP_2543 RSP_2543 CDS None chromosome 1 1186682 1187881 - Peptidoglycan-binding LysM (possible peptidase) (NCBI) False
RSP_2705 pyrH CDS None chromosome 1 1354336 1355076 + Uridylate kinase (NCBI) False
RSP_2706 frr CDS None chromosome 1 1355162 1355728 + Ribosome recycling factor (NCBI) False
RSP_2710 RSP_2710 CDS None chromosome 1 1358559 1359893 + Putative membrane-associated zinc metalloprotease (NCBI) False
RSP_2711 RSP_2711 CDS None chromosome 1 1360291 1362690 + putative outer membrane protein (NCBI) False
RSP_2956 tktA CDS None chromosome 1 1637358 1639376 + Transketolase (NCBI) False
RSP_2959 gapB CDS None chromosome 1 1641318 1642319 + Glyceraldehyde 3-phosphate dehydrogenase B (GAPDH) (NCBI) False
RSP_3177 fabB CDS None chromosome 2 229489 230718 - 3-oxoacyl-(Acyl-carrier-protein) synthase (NCBI) False
RSP_3178 fabA CDS None chromosome 2 230738 231247 - 3-hydroxydecanoyl-(acyl-carrier-protein) dehydratase (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 360

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.