Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 363 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 363

There are 6 regulatory influences for Module 363

Regulator Table (6)
Regulator Name Type
RSP_2591 tf
RSP_1163 tf
RSP_0755 tf
RSP_3341 tf
RSP_0402 tf
RSP_1704 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
8424 3.40e-09 AAAtTaAAactGAAaGAcCaATcT
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8425 2.40e-01 AAGcGGcTGAcccaaGGacGGAcG
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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 363 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 1.87e-02 4.01e-02 4/27
Pentose and glucuronate interconversions kegg pathway 9.00e-06 1.57e-04 3/27
Lipid Metabolism kegg subcategory 1.26e-04 1.42e-03 4/27
Fatty acid biosynthesis kegg pathway 1.10e-05 1.87e-04 3/27
Environmental Information Processing kegg category 9.11e-04 5.83e-03 7/27
Membrane Transport kegg subcategory 1.51e-02 3.42e-02 4/27
ABC transporters kegg pathway 9.09e-03 2.44e-02 4/27
Signal Transduction kegg subcategory 4.13e-03 1.47e-02 3/27
Two-component system kegg pathway 4.13e-03 1.47e-02 3/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 1.00e-06 4.00e-06 6/27
Carbohydrates, organic alcohols, and acids tigr sub1role 0.00e+00 0.00e+00 6/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 2.30e-05 7.60e-05 19/27
Carbohydrate transport and metabolism cog subcategory 0.00e+00 0.00e+00 10/27
Lipid transport and metabolism cog subcategory 2.00e-06 7.00e-06 7/27
Secondary metabolites biosynthesis, transport and catabolism cog subcategory 3.95e-04 7.94e-04 4/27
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 363

There are 27 genes in Module 363

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0099 RSP_0099 CDS None chromosome 1 1811327 1811941 - TRAP-T family sorbitol/mannitol transporter, DctQ (4TMs) subunit (NCBI) False
RSP_0490 RSP_0490 CDS None chromosome 1 2223935 2224687 + carbohydrate kinase (NCBI) False
RSP_0910 dctP CDS None chromosome 1 2659690 2660694 + TRAP-T family transporter, C4-dicarboxylate-binding protein DctP (NCBI) False
RSP_0911 dctQ CDS None chromosome 1 2660780 2661463 + TRAP-T family C4-dicarboxylate transporter, DctQ (4TMs) subunit (NCBI) False
RSP_0912 dctM CDS None chromosome 1 2661465 2662790 + TRAP-T family C4-dicarboxylate transporter, DctM (12TMs) subunit (NCBI) False
RSP_1041 RSP_1041 CDS None chromosome 1 2802063 2803568 - Malonyl CoA synthetase (NCBI) False
RSP_1176 xylA CDS None chromosome 1 2943689 2944990 - Xylose isomerase (NCBI) False
RSP_1177 xylB CDS None chromosome 1 2944987 2946423 - Xylulose kinase (NCBI) False
RSP_1178 RSP_1178 CDS None chromosome 1 2946423 2947205 - ABC sugar (xylose) transporter, ATPase subunit (NCBI) False
RSP_1179 xylH CDS None chromosome 1 2947202 2948500 - ABC sugar (xylose) transporter, inner membrane subunit (NCBI) False
RSP_1180 xylF CDS None chromosome 1 2948588 2949613 - ABC sugar (xylose) transporter, periplasmic binding protein (NCBI) False
RSP_1181 xylR CDS None chromosome 1 2949805 2951082 + xylose operon repressor (NCBI) False
RSP_1599 RSP_1599 CDS None chromosome 1 196087 197736 - AMP-binding protein (NCBI) False
RSP_1912 RSP_1912 CDS None chromosome 1 510817 511056 - hypothetical protein (NCBI) False
RSP_1913 RSP_1913 CDS None chromosome 1 511100 511729 - 3-oxoadipate CoA-transferase, beta subunit (NCBI) False
RSP_1914 RSP_1914 CDS None chromosome 1 511745 512443 - 3-ketoacid CoA transferase alpha subunit (NCBI) False
RSP_2582 RSP_2582 CDS None chromosome 1 1226181 1227290 + hypothetical protein (NCBI) False
RSP_2584 RSP_2584 CDS None chromosome 1 1228300 1228743 + hypothetical protein (NCBI) False
RSP_2585 RSP_2585 CDS None chromosome 1 1228759 1229007 + hypothetical protein (NCBI) False
RSP_2586 RSP_2586 CDS None chromosome 1 1229004 1229732 + ABC multidrug efflux transporter, ATPase subunit (NCBI) False
RSP_2587 RSP_2587 CDS None chromosome 1 1229729 1230589 + ABC multidrug efflux transporter, inner membrane subunit (NCBI) False
RSP_2588 RSP_2588 CDS None chromosome 1 1230599 1231192 + hypothetical protein (NCBI) False
RSP_2591 flhR CDS None chromosome 1 1233459 1234166 + two component transcriptional regulator, LuxR family family (NCBI) True
RSP_3176 fabI CDS None chromosome 2 228690 229478 - enoyl-(acyl-carrier protein) reductase (NADH) (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
RSP_3179 fur CDS None chromosome 2 231397 231837 + probable Ferric-uptake regulator (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 363

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.